Variant report

Variant	rs3762607
Chromosome Location	chr4:46996338-46996339
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	CEBPB	chr4:46996198-46996533	IMR90	lung:	n/a	n/a
2	MAX	chr4:46995286-46996357	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr4:46996208-46996468	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
GABRA4	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10517171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10517172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10517173	0.86[AMR][1000 genomes]
rs10517174	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MKK][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10517175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11727160	0.88[EUR][1000 genomes]
rs11727163	0.86[AMR][1000 genomes]
rs11729000	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729961	0.86[EUR][1000 genomes]
rs11731576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11732239	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11732398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12512719	0.86[EUR][1000 genomes]
rs16851647	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16859823	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16859826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16859842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2280072	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3762608	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762610	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4695182	0.82[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs4695183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4695184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57314699	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59115556	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59481829	0.86[EUR][1000 genomes]
rs59675437	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61409453	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73813760	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73813761	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73813771	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73813772	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73813773	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470031	chr4:46982218-47006399	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
2	esv3431136	chr4:46995950-46996470	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:46993400-46997400	Active TSS	Brain Angular Gyrus	brain
2	chr4:46993400-46997600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:46994000-46997400	Active TSS	Brain Anterior Caudate	brain
4	chr4:46994200-46996400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr4:46994400-46996600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:46994400-46996600	Bivalent/Poised TSS	Fetal Brain Female	brain
7	chr4:46994600-46996600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:46994800-46996600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr4:46994800-46996600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:46994800-46996600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr4:46994800-46996600	Active TSS	Fetal Heart	heart
12	chr4:46994800-46997000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:46995000-46996400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:46995000-46996400	Bivalent/Poised TSS	Colonic Mucosa	Colon
15	chr4:46995000-46996400	Flanking Bivalent TSS/Enh	NH-A	brain
16	chr4:46995000-46996600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:46995000-46996600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr4:46995000-46996600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:46995000-46996600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:46995000-46996800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr4:46995000-46996800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr4:46995200-46996400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:46995200-46996400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:46995200-46996400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:46995200-46996400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:46995200-46996400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:46995200-46996400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:46995200-46996400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:46995200-46996400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr4:46995200-46996400	Bivalent/Poised TSS	Fetal Thymus	thymus
31	chr4:46995200-46996400	Active TSS	Right Atrium	heart
32	chr4:46995200-46996400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr4:46995200-46996600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr4:46995200-46996800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr4:46995400-46996400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr4:46995400-46996400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:46995400-46996400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:46995400-46996400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr4:46995400-46996400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
40	chr4:46995400-46996400	Bivalent Enhancer	Psoas Muscle	Psoas
41	chr4:46995400-46996400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
42	chr4:46995400-46996400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
43	chr4:46995400-46996400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
44	chr4:46995600-46996400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
45	chr4:46995600-46996400	Bivalent Enhancer	Adipose Nuclei	Adipose
46	chr4:46995600-46996400	Active TSS	Aorta	Aorta
47	chr4:46995600-46996400	Active TSS	Esophagus	oesophagus
48	chr4:46995600-46996400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
49	chr4:46995600-46996400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr4:46995600-46996400	Bivalent Enhancer	Ovary	ovary

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