Variant report

Variant	rs4989124
Chromosome Location	chr7:102101510-102101511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:102101262-102101512	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102096270..102098685-chr7:102100293..102102957,2	K562	blood:
2	chr7:102100941..102102997-chr7:102104685..102106440,2	MCF-7	breast:
3	chr7:102073812..102076569-chr7:102099712..102102534,2	K562	blood:

Variant related genes	Relation type
LRWD1	TF binding region
MIR5090	TF binding region
ENSG00000160993	Chromatin interaction
ENSG00000161036	Chromatin interaction
ENSG00000239480	Chromatin interaction
ENSG00000266715	Chromatin interaction
ENSG00000160991	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1131383	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11764413	0.82[TSI][hapmap]
rs4543479	0.82[TSI][hapmap]
rs55981184	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62483804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1814780	chr7:101912320-102375950	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv1819566	chr7:101912320-102375950	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1822347	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv1825708	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv1842898	chr7:101912320-102375950	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	esv1847418	chr7:101912320-102375950	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv427798	chr7:101912320-102375950	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv428182	chr7:101912320-102375950	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
10	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
11	nsv1029079	chr7:101939998-102112371	Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
12	esv1818954	chr7:101957513-102328097	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	esv1828190	chr7:101966669-102439077	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	esv1829377	chr7:101970299-102330884	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv831083	chr7:101981005-102295869	Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
16	esv1806297	chr7:101981544-102330884	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	esv1810415	chr7:101993063-102375950	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	esv1811751	chr7:101993063-102375950	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	esv1829118	chr7:101993063-102375950	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	esv1833155	chr7:101993063-102375950	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
21	esv1832541	chr7:102072448-102328097	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
22	nsv1025363	chr7:102072448-102471485	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
23	esv1803868	chr7:102080919-102109591	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
24	nsv888831	chr7:102082286-102274889	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
25	esv1817154	chr7:102083909-102329872	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
26	esv1847127	chr7:102085576-102329872	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
27	esv1822399	chr7:102085576-102335217	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
28	nsv888832	chr7:102087202-102183897	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
29	esv1796247	chr7:102087750-102327899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
30	nsv5879	chr7:102090768-102387803	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
31	nsv8192	chr7:102091052-102333199	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
32	nsv607999	chr7:102091735-102113899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
33	esv1833186	chr7:102094908-102337526	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
34	nsv888833	chr7:102101269-102334106	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4989124	AC093668.2	cis	Artery Tibial	GTEx
rs4989124	NPTX2	cis	parietal	SCAN
rs4989124	POLR2J	cis	multi-tissue	Pritchard
rs4989124	POLR2J	Cis_1M	lymphoblastoid	RTeQTL
rs4989124	LRWD1	cis	multi-tissue	Pritchard
rs4989124	ALKBH4	cis	parietal	SCAN
rs4989124	RASA4DP	cis	Muscle Skeletal	GTEx
rs4989124	AC093668.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4989124	AC093668.2	cis	Thyroid	GTEx
rs4989124	AC093668.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102075000-102104000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:102075200-102104200	Weak transcription	Fetal Kidney	kidney
3	chr7:102075600-102103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:102075800-102103600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:102076000-102104200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:102081200-102104200	Weak transcription	Right Atrium	heart
7	chr7:102084400-102104000	Weak transcription	Fetal Brain Male	brain
8	chr7:102088200-102104200	Weak transcription	HUVEC	blood vessel
9	chr7:102088400-102104000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:102092400-102104200	Weak transcription	Psoas Muscle	Psoas
11	chr7:102092400-102104200	Weak transcription	Stomach Mucosa	stomach
12	chr7:102092400-102104200	Weak transcription	A549	lung
13	chr7:102092400-102104200	Weak transcription	HSMM	muscle
14	chr7:102092400-102104200	Weak transcription	NHDF-Ad	bronchial
15	chr7:102092600-102104000	Weak transcription	HSMMtube	muscle
16	chr7:102092600-102104200	Weak transcription	HMEC	breast
17	chr7:102092600-102104200	Weak transcription	NHEK	skin
18	chr7:102093800-102101600	Strong transcription	Fetal Brain Female	brain
19	chr7:102093800-102102800	Strong transcription	Fetal Intestine Small	intestine
20	chr7:102094800-102103400	Strong transcription	Fetal Stomach	stomach
21	chr7:102095200-102101600	Strong transcription	Fetal Muscle Leg	muscle
22	chr7:102095200-102101800	Strong transcription	Primary T cells from cord blood	blood
23	chr7:102095200-102103400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:102095600-102102600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:102095600-102102600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:102097800-102104000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:102097800-102104200	Weak transcription	NH-A	brain
28	chr7:102098400-102104000	Weak transcription	GM12878-XiMat	blood
29	chr7:102098600-102104200	Weak transcription	Hela-S3	cervix
30	chr7:102098800-102104000	Weak transcription	Colon Smooth Muscle	Colon
31	chr7:102098800-102104200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:102098800-102104200	Weak transcription	Colonic Mucosa	Colon
33	chr7:102098800-102104200	Weak transcription	K562	blood
34	chr7:102098800-102104400	Weak transcription	Small Intestine	intestine
35	chr7:102099000-102104000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:102099000-102104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:102099000-102104200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:102099000-102104200	Weak transcription	Primary B cells from cord blood	blood
39	chr7:102099000-102104200	Weak transcription	NHLF	lung
40	chr7:102099200-102104000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:102099200-102104000	Weak transcription	HepG2	liver
42	chr7:102099400-102104200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr7:102099600-102104200	Weak transcription	Osteobl	bone
44	chr7:102100000-102103200	Weak transcription	Brain Anterior Caudate	brain
45	chr7:102100000-102104000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr7:102100000-102104000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:102100000-102104000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:102100000-102104000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:102100000-102104000	Weak transcription	Pancreas	Pancrea
50	chr7:102100000-102104200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links