Variant report

Variant	rs3747690
Chromosome Location	chr4:48988450-48988451
allele	A/C
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	CTCF	chr4:48988400-48988550	WERI-Rb-1	eye:	n/a	n/a
2	CTBP2	chr4:48987811-48989013	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr4:48988326-48988564	H1-hESC	embryonic stem cell:	n/a	chr4:48988371-48988381
4	ZNF143	chr4:48987955-48988481	H1-hESC	embryonic stem cell:	n/a	chr4:48988375-48988385
5	CTCF	chr4:48988340-48988561	H1-hESC	embryonic stem cell:	n/a	chr4:48988371-48988381
6	E2F6	chr4:48987909-48988595	H1-hESC	embryonic stem cell:	n/a	chr4:48988361-48988373 chr4:48988359-48988369 chr4:48988318-48988330 chr4:48988132-48988143
7	CTCF	chr4:48987885-48988628	H1-hESC	embryonic stem cell:	n/a	chr4:48988371-48988381
8	CTCF	chr4:48988399-48988561	NHEK	skin:	n/a	n/a
9	RAD21	chr4:48988230-48988666	H1-hESC	embryonic stem cell:	n/a	chr4:48988372-48988382 chr4:48988371-48988380
10	CTCF	chr4:48988440-48988590	WERI-Rb-1	eye:	n/a	n/a
11	RAD21	chr4:48987783-48988753	H1-hESC	embryonic stem cell:	n/a	chr4:48988372-48988382 chr4:48988371-48988380
12	GABPA	chr4:48987971-48988493	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr4:48988420-48988570	HRE	kidney:	n/a	n/a
14	TBP	chr4:48987942-48988472	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr4:48987906-48988672	H1-hESC	embryonic stem cell:	n/a	chr4:48988372-48988382 chr4:48988371-48988380

Variant related genes	Relation type
CWH43	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2605232	1.00[ASW][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs2768948	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs6811205	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription 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	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv1004364	chr4:48961611-49083089	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv1798238	chr4:48979634-48993377	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1819278	chr4:48979634-48993377	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1839152	chr4:48979634-48993377	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv441875	chr4:48979634-48993377	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3747690	GABRG1	cis	cerebellum	SCAN
rs3747690	TEC	cis	parietal	SCAN
rs3747690	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48987600-48988600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
2	chr4:48987600-48988600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:48987600-48988800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:48987600-48988800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:48987600-48988800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:48987600-48988800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:48987600-48988800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:48987600-48988800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:48987600-48989200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:48987600-48989200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:48987800-48988600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr4:48987800-48988600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr4:48987800-48988600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:48987800-48988600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:48987800-48988600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
16	chr4:48987800-48988600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:48987800-48988600	Bivalent Enhancer	Adipose Nuclei	Adipose
18	chr4:48987800-48988600	Flanking Active TSS	Esophagus	oesophagus
19	chr4:48987800-48988600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr4:48987800-48988600	Bivalent Enhancer	Lung	lung
21	chr4:48987800-48988600	Flanking Bivalent TSS/Enh	HMEC	breast
22	chr4:48987800-48988800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:48987800-48988800	Enhancers	Pancreas	Pancrea
24	chr4:48987800-48989000	Bivalent Enhancer	Fetal Brain Male	brain
25	chr4:48987800-48989800	Active TSS	Rectal Smooth Muscle	rectum
26	chr4:48988000-48988600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:48988000-48988600	Bivalent Enhancer	Brain Angular Gyrus	brain
28	chr4:48988000-48988600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
29	chr4:48988000-48988600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr4:48988000-48988600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
31	chr4:48988000-48988600	Bivalent Enhancer	Spleen	Spleen
32	chr4:48988000-48988800	Bivalent/Poised TSS	Stomach Mucosa	stomach
33	chr4:48988000-48989200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr4:48988200-48988600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
35	chr4:48988200-48988600	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr4:48988200-48988600	Active TSS	Gastric	stomach
37	chr4:48988200-48988600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
38	chr4:48988200-48989200	Bivalent/Poised TSS	NHEK	skin
39	chr4:48988200-48990000	Active TSS	Colonic Mucosa	Colon
40	chr4:48988400-48988600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:48988400-48988600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
42	chr4:48988400-48988600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:48988400-48988600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:48988400-48988600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:48988400-48988600	Flanking Active TSS	Liver	Liver
46	chr4:48988400-48988600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
47	chr4:48988400-48988600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:48988400-48988600	Bivalent/Poised TSS	Psoas Muscle	Psoas
49	chr4:48988400-48988600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr4:48988400-48988600	Bivalent/Poised TSS	Right Ventricle	heart

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