Variant report

Variant	rs7637968
Chromosome Location	chr3:23904969-23904970
allele	C/T
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	GATA2	chr3:23904461-23905044	HUVEC	blood vessel:	n/a	n/a
2	GATA3	chr3:23904367-23905042	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:23904476-23904995	HUVEC	blood vessel:	n/a	n/a
4	GATA3	chr3:23904533-23904973	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23845333..23847411-chr3:23904477..23906192,2	K562	blood:
2	chr3:23902696..23905210-chr3:23958576..23960216,2	MCF-7	breast:

Variant related genes	Relation type
UBE2E1	TF binding region
ENSG00000174748	Chromatin interaction
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1133926	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs1136155	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11710679	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11711380	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11713246	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs11718625	1.00[GIH][hapmap];0.82[JPT][hapmap]
rs11922577	0.86[MEX][hapmap]
rs11922609	0.81[CHD][hapmap]
rs12497944	0.82[JPT][hapmap]
rs13318927	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13325754	0.92[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs17787211	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2001209	0.81[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs28623591	0.93[EUR][1000 genomes]
rs34476593	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4131864	0.82[JPT][hapmap]
rs61645368	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6550809	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6778970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6779537	0.81[AFR][1000 genomes]
rs6787216	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6789983	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6800407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72627066	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73825116	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73825124	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825170	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825178	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73825181	0.85[EUR][1000 genomes]
rs7629325	0.84[EUR][1000 genomes]
rs8933	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9815334	0.93[EUR][1000 genomes]
rs9834166	0.84[EUR][1000 genomes]
rs9836860	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9836970	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs9850255	0.91[EUR][1000 genomes]
rs9857442	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9876561	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7637968	ZNF385D	cis	parietal	SCAN
rs7637968	NKIRAS1	cis	cerebellum	SCAN
rs7637968	NR1D2	cis	multi-tissue	Pritchard
rs7637968	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs7637968	NKIRAS1	cis	parietal	SCAN
rs7637968	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23876800-23906800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:23879000-23907400	Weak transcription	K562	blood
3	chr3:23882200-23905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:23882800-23906000	Weak transcription	HepG2	liver
5	chr3:23893600-23906400	Weak transcription	Aorta	Aorta
6	chr3:23893600-23906600	Weak transcription	Colonic Mucosa	Colon
7	chr3:23898200-23907000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:23898400-23907200	Weak transcription	Stomach Mucosa	stomach
9	chr3:23899000-23907000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:23899400-23905600	Weak transcription	Liver	Liver
11	chr3:23899400-23906200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:23899400-23906200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:23899400-23907000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:23899400-23907200	Weak transcription	NH-A	brain
15	chr3:23900800-23906200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:23900800-23906200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:23900800-23907000	Weak transcription	Fetal Kidney	kidney
18	chr3:23901000-23905400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:23901000-23905600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:23901000-23905600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:23901000-23906000	Weak transcription	NHLF	lung
22	chr3:23901000-23906400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:23901000-23906800	Weak transcription	NHDF-Ad	bronchial
24	chr3:23901000-23907400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:23901200-23906200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:23901200-23906200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:23901200-23906400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:23901200-23906400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:23901200-23906400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:23901200-23906400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:23901200-23906400	Weak transcription	Gastric	stomach
32	chr3:23901200-23906600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:23901200-23907000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:23901200-23907200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:23901200-23907200	Weak transcription	HMEC	breast
36	chr3:23901200-23907400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:23901200-23914800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:23901200-23915400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:23901200-23915400	Weak transcription	HSMM	muscle
40	chr3:23901200-23942000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:23901400-23906200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:23901400-23906400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:23901400-23906400	Weak transcription	Placenta	Placenta
44	chr3:23901400-23906800	Weak transcription	Small Intestine	intestine
45	chr3:23901400-23907000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:23901400-23915200	Weak transcription	NHEK	skin
47	chr3:23901600-23906200	Weak transcription	Right Atrium	heart
48	chr3:23901600-23906600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:23901600-23906600	Weak transcription	HSMMtube	muscle
50	chr3:23901800-23906200	Weak transcription	Ovary	ovary

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