Variant report

Variant	rs1626813
Chromosome Location	chr4:2819063-2819064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr4:2819036-2820110	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:2818755-2819063	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2818050..2820446-chr4:2931198..2934919,4	MCF-7	breast:
2	chr4:2818330..2820965-chr4:2936129..2938646,4	MCF-7	breast:
3	chr4:2793845..2803067-chr4:2816443..2823671,22	MCF-7	breast:
4	chr4:2818848..2822289-chr4:2843327..2846796,5	MCF-7	breast:
5	chr4:2818530..2821169-chr4:2881997..2885134,3	K562	blood:
6	chr4:2818404..2821312-chr4:2845258..2848491,3	MCF-7	breast:
7	chr4:2815294..2817110-chr4:2817843..2820313,2	K562	blood:
8	chr4:2794084..2803742-chr4:2816227..2824357,23	MCF-7	breast:
9	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:

No data

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1623454	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs1709003	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1751848	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap]
rs1784148	0.92[CEU][hapmap];0.81[CHD][hapmap]
rs1784149	0.92[CEU][hapmap]
rs1794395	0.88[ASN][1000 genomes]
rs189139	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2239727	0.89[ASN][1000 genomes]
rs231339	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs231396	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs231399	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs231402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs382379	0.91[CHB][hapmap]
rs743691	0.83[CHB][hapmap]
rs9684650	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
9	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1626813	GRK4	cis	parietal	SCAN
rs1626813	ADD1	cis	lymphoblastoid	seeQTL
rs1626813	NAT8L	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:2811800-2819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:2814800-2819200	Weak transcription	NH-A	brain
4	chr4:2814800-2819400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:2815200-2819200	Weak transcription	Small Intestine	intestine
6	chr4:2815200-2819200	Weak transcription	NHLF	lung
7	chr4:2815400-2819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:2815400-2819200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:2815400-2819200	Weak transcription	HSMM	muscle
10	chr4:2815400-2819200	Weak transcription	HSMMtube	muscle
11	chr4:2815400-2819600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:2815600-2819200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:2815600-2819200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:2815600-2819200	Weak transcription	Fetal Brain Male	brain
15	chr4:2815600-2819200	Weak transcription	Right Atrium	heart
16	chr4:2815600-2819400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:2815600-2819600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:2815600-2819600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:2815600-2819600	Weak transcription	Fetal Kidney	kidney
20	chr4:2815600-2821600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:2815800-2821800	Weak transcription	HepG2	liver
22	chr4:2815800-2827000	Weak transcription	Fetal Heart	heart
23	chr4:2817400-2819800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr4:2817600-2819200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr4:2817800-2820000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:2817800-2820400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr4:2818000-2819800	Enhancers	Stomach Mucosa	stomach
28	chr4:2818400-2819200	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:2818400-2819200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:2818400-2819200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:2818400-2819400	Enhancers	Primary B cells from peripheral blood	blood
32	chr4:2818400-2819600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:2818400-2819600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr4:2818600-2819200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:2818600-2819200	Enhancers	Fetal Muscle Leg	muscle
36	chr4:2818600-2819400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:2818600-2819400	Enhancers	Brain Hippocampus Middle	brain
38	chr4:2818600-2819400	Enhancers	Fetal Thymus	thymus
39	chr4:2818600-2819400	Weak transcription	Osteobl	bone
40	chr4:2818600-2819600	Enhancers	Primary B cells from cord blood	blood
41	chr4:2818600-2819600	Weak transcription	Brain Anterior Caudate	brain
42	chr4:2818600-2819800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr4:2818600-2820000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr4:2818600-2820200	Enhancers	Spleen	Spleen
45	chr4:2818800-2819200	Enhancers	Fetal Intestine Large	intestine
46	chr4:2818800-2819200	Enhancers	Fetal Muscle Trunk	muscle
47	chr4:2818800-2819400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
48	chr4:2818800-2819400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:2818800-2819400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:2818800-2819400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links