Variant report

Variant	rs10937780
Chromosome Location	chr4:7048842-7048843
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	NFYB	chr4:7048795-7049139	GM12878	blood:	n/a	chr4:7048951-7048966 chr4:7048952-7048966 chr4:7048951-7048966 chr4:7048953-7048966
2	NFYB	chr4:7048786-7049044	K562	blood:	n/a	chr4:7048951-7048966 chr4:7048952-7048966 chr4:7048951-7048966 chr4:7048953-7048966
3	WRNIP1	chr4:7048766-7048956	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:6912685..6914453-chr4:7047994..7050583,2	MCF-7	breast:
2	chr4:7034052..7036978-chr4:7048752..7050371,2	MCF-7	breast:
3	chr4:7041999..7051916-chr4:7066728..7075643,37	MCF-7	breast:
4	chr4:7047952..7049903-chr4:7053524..7056109,2	MCF-7	breast:
5	chr4:7042421..7051559-chr4:7062214..7072674,24	MCF-7	breast:

Variant related genes	Relation type
CCDC96	TF binding region
ENSG00000245748	TF binding region
ENSG00000173011	Chromatin interaction
ENSG00000109519	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10937778	0.90[ASW][hapmap]
rs10937779	0.90[ASW][hapmap]
rs11931598	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs28385900	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28661210	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4689581	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs870660	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv878533	chr4:7032180-7063524	Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv4217	chr4:7035512-7080230	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	esv1801315	chr4:7044007-7052777	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv1835149	chr4:7044007-7052777	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv593556	chr4:7044447-7048842	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv1798014	chr4:7044504-7052182	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10937780	SLC2A9	cis	parietal	SCAN
rs10937780	GRPEL1	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7045800-7049400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr4:7046200-7068600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7046400-7049000	Flanking Active TSS	GM12878-XiMat	blood
4	chr4:7046400-7049800	Enhancers	Primary B cells from peripheral blood	blood
5	chr4:7046400-7049800	Genic enhancers	Spleen	Spleen
6	chr4:7046600-7049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:7046600-7050400	Enhancers	Lung	lung
8	chr4:7046600-7050800	Genic enhancers	Fetal Muscle Leg	muscle
9	chr4:7046600-7051400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:7046600-7053800	Weak transcription	A549	lung
11	chr4:7046600-7055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:7046600-7055600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:7046600-7055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:7046600-7062600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:7046800-7049000	Enhancers	Fetal Thymus	thymus
16	chr4:7046800-7049200	Enhancers	HSMMtube	muscle
17	chr4:7046800-7049400	Enhancers	Liver	Liver
18	chr4:7046800-7049400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
19	chr4:7046800-7049800	Enhancers	Left Ventricle	heart
20	chr4:7046800-7050000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:7046800-7050000	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr4:7046800-7050000	Enhancers	Psoas Muscle	Psoas
23	chr4:7046800-7062000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:7047000-7049400	Enhancers	Colonic Mucosa	Colon
25	chr4:7047000-7049400	Enhancers	Ovary	ovary
26	chr4:7047000-7049400	Enhancers	Right Ventricle	heart
27	chr4:7047000-7049600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:7047000-7049800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr4:7047000-7049800	Enhancers	Right Atrium	heart
30	chr4:7047000-7050000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:7047000-7053000	Weak transcription	NHLF	lung
32	chr4:7047000-7056000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:7047000-7056200	Weak transcription	HUVEC	blood vessel
34	chr4:7047000-7057400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:7047000-7059600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:7047000-7061200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:7047200-7049400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr4:7047200-7049400	Genic enhancers	Primary T cells from cord blood	blood
39	chr4:7047200-7049400	Enhancers	Fetal Heart	heart
40	chr4:7047200-7049800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr4:7047200-7055600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:7047200-7056200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:7047200-7059600	Weak transcription	NH-A	brain
44	chr4:7047400-7049000	Genic enhancers	Fetal Brain Female	brain
45	chr4:7047400-7050000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:7047400-7059200	Strong transcription	Fetal Intestine Small	intestine
47	chr4:7047400-7062400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:7047600-7049000	Strong transcription	Fetal Intestine Large	intestine
49	chr4:7047600-7049400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:7047600-7049400	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links