Variant report

Variant	rs809639
Chromosome Location	chr2:233731244-233731245
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233713450..233715209-chr2:233729940..233731619,2	K562	blood:
2	chr2:233730563..233732599-chr2:233735089..233737149,2	K562	blood:
3	chr2:233715218..233716776-chr2:233729357..233731524,2	MCF-7	breast:
4	chr2:233727449..233731351-chr2:233736566..233741117,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1022330	0.85[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10933411	0.96[ASN][1000 genomes]
rs10933412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11555646	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11676216	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11679079	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12474040	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12694917	0.96[ASN][1000 genomes]
rs12990821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13003675	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13004406	0.85[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs13011298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13013142	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1446308	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446310	0.85[ASN][1000 genomes]
rs1446311	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs1801251	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1867778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1947105	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs2012221	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2044449	0.98[ASN][1000 genomes]
rs2100053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2197563	0.83[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2250654	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250665	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305137	0.96[ASN][1000 genomes]
rs2305141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2592102	0.98[ASN][1000 genomes]
rs2592113	0.85[ASN][1000 genomes]
rs2592115	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592116	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592117	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592126	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2674839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2675957	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2675966	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675971	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2675973	0.96[ASN][1000 genomes]
rs2675974	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs283466	0.85[ASN][1000 genomes]
rs283468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs283469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs283471	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs283474	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs283475	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs283476	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs283486	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs3816334	0.96[ASN][1000 genomes]
rs3817311	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs4973053	0.85[ASN][1000 genomes]
rs4973054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4973055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4973056	0.95[ASN][1000 genomes]
rs4973560	0.83[ASN][1000 genomes]
rs4973561	0.85[ASN][1000 genomes]
rs6437074	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs6704768	0.81[JPT][hapmap]
rs6714245	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6717841	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6719061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6738386	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6745879	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6746294	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6747645	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs6748027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs709933	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709938	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737028	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7558609	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs7568385	0.81[ASN][1000 genomes]
rs7573208	0.87[ASN][1000 genomes]
rs7587309	0.95[ASN][1000 genomes]
rs7589201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7606090	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs778166	0.80[ASN][1000 genomes]
rs778338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778339	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778340	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778368	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs9653383	0.84[ASN][1000 genomes]
rs991873	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs809639	HMGB3L1	trans	parietal	SCAN
rs809639	C2orf82	cis	Temporal Cortex	GTEx
rs809639	C2orf82	cis	parietal	SCAN
rs809639	C2orf82	cis	Frontal Cortex	GTEx
rs809639	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233722800-233738000	Weak transcription	Stomach Mucosa	stomach
3	chr2:233723000-233733200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:233723000-233740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:233723200-233733200	Weak transcription	Small Intestine	intestine
6	chr2:233723200-233736600	Weak transcription	Colonic Mucosa	Colon
7	chr2:233723200-233738600	Weak transcription	K562	blood
8	chr2:233723600-233734200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:233723600-233735200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:233723600-233736400	Weak transcription	Right Ventricle	heart
11	chr2:233723600-233736600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:233724000-233734600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:233724000-233736000	Weak transcription	Fetal Brain Male	brain
14	chr2:233724200-233732200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:233724200-233733800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:233724200-233738600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:233724400-233734200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:233724600-233734200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:233724600-233738600	Weak transcription	Esophagus	oesophagus
20	chr2:233724800-233732800	Weak transcription	Hela-S3	cervix
21	chr2:233724800-233734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:233725000-233735800	Weak transcription	Fetal Thymus	thymus
23	chr2:233726000-233733400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:233726000-233737400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:233726000-233740400	Weak transcription	HMEC	breast
26	chr2:233726200-233735000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:233726200-233735600	Weak transcription	Osteobl	bone
28	chr2:233726200-233737400	Weak transcription	Fetal Brain Female	brain
29	chr2:233726400-233731400	Weak transcription	Ovary	ovary
30	chr2:233726400-233732200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:233726400-233732400	Weak transcription	Fetal Kidney	kidney
32	chr2:233726400-233733000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:233726400-233734400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:233726400-233735000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:233726400-233735000	Weak transcription	Spleen	Spleen
36	chr2:233726400-233736000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:233726400-233736200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:233726400-233736200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:233726400-233738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:233726400-233739000	Weak transcription	Thymus	Thymus
41	chr2:233726400-233740200	Weak transcription	Primary B cells from cord blood	blood
42	chr2:233726400-233740400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:233726400-233740800	Weak transcription	HSMM	muscle
44	chr2:233726600-233731400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:233726600-233732200	Weak transcription	Adipose Nuclei	Adipose
46	chr2:233726600-233734000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:233726600-233734000	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:233726600-233734600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:233726600-233734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:233726600-233735800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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