Variant report

Variant	rs6809251
Chromosome Location	chr3:196338875-196338876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196338663..196341923-chr3:196355060..196359502,4	K562	blood:
2	chr3:196338343..196339261-chr3:196411534..196412124,2	K562	blood:
3	chr3:196330580..196333990-chr3:196334226..196339571,6	K562	blood:
4	chr3:196336450..196339251-chr3:196363480..196365260,2	K562	blood:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11185550	0.82[AMR][1000 genomes]
rs11719820	0.86[ASN][1000 genomes]
rs12718060	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075023	0.87[ASN][1000 genomes]
rs13075160	0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1973264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916530	0.83[AMR][1000 genomes]
rs6763582	0.88[ASN][1000 genomes]
rs6798553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7629845	0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7634344	0.87[AMR][1000 genomes]
rs9858309	0.88[AMR][1000 genomes]
rs9868705	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9883029	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
10	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6809251	FAM43A	cis	parietal	SCAN
rs6809251	TCTEX1D2	cis	cerebellum	SCAN
rs6809251	LOC401109	cis	cerebellum	SCAN
rs6809251	PPP1R2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196331800-196339000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:196331800-196339200	Weak transcription	Right Atrium	heart
3	chr3:196336000-196339200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:196336000-196340200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:196336200-196339800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr3:196336200-196339800	Enhancers	Placenta	Placenta
7	chr3:196336200-196341000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:196336400-196339200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:196336400-196339800	Enhancers	Adipose Nuclei	Adipose
10	chr3:196336600-196339000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:196336600-196339200	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:196336800-196339000	Enhancers	Fetal Thymus	thymus
13	chr3:196336800-196339200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:196336800-196345800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:196337000-196339000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:196337000-196339000	Weak transcription	Fetal Intestine Small	intestine
17	chr3:196337000-196339000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:196337000-196339200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:196337000-196347000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:196337200-196339000	Weak transcription	Primary B cells from cord blood	blood
21	chr3:196337200-196339000	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:196337200-196339000	Weak transcription	Spleen	Spleen
23	chr3:196337200-196339200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:196337200-196339200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:196337200-196339600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:196337200-196340400	Weak transcription	Left Ventricle	heart
27	chr3:196337200-196347000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:196337400-196339000	Weak transcription	Colonic Mucosa	Colon
29	chr3:196337400-196339000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:196337400-196339200	Weak transcription	Lung	lung
31	chr3:196337800-196340400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:196338000-196339000	Enhancers	Primary T cells from cord blood	blood
33	chr3:196338000-196339600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:196338000-196339800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:196338400-196339000	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:196338400-196339200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr3:196338400-196339400	Enhancers	Colon Smooth Muscle	Colon
38	chr3:196338400-196339600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:196338400-196339800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr3:196338400-196339800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr3:196338400-196339800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:196338400-196339800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:196338400-196339800	Enhancers	Thymus	Thymus
44	chr3:196338600-196339000	Enhancers	Rectal Smooth Muscle	rectum
45	chr3:196338600-196339000	Enhancers	K562	blood
46	chr3:196338600-196339400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:196338600-196339600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:196338600-196339800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:196338600-196339800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:196338600-196339800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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