Variant report

Variant	rs3777754
Chromosome Location	chr6:12160547-12160548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12158453..12160780-chr6:12288410..12290344,2	MCF-7	breast:
2	chr6:12159346..12162270-chr6:12162477..12165476,3	K562	blood:
3	chr6:12132489..12134557-chr6:12159288..12161389,2	K562	blood:
4	chr6:12151617..12154560-chr6:12159442..12161987,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10498679	0.88[CEU][hapmap]
rs1126472	0.86[JPT][hapmap]
rs12176308	0.88[CEU][hapmap]
rs16872277	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228220	0.86[JPT][hapmap]
rs3734271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs3777758	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777770	0.86[JPT][hapmap]
rs3777771	0.86[JPT][hapmap]
rs3777773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55718117	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905883	0.92[YRI][hapmap]
rs6907440	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910959	0.88[CEU][hapmap]
rs6916455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6928420	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs6940075	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs72826076	0.82[EUR][1000 genomes]
rs72826081	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72826086	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826088	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826091	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296253	0.86[CEU][hapmap]
rs9296262	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs9349095	0.88[CEU][hapmap]
rs9357278	1.00[CEU][hapmap]
rs9366970	0.88[CEU][hapmap]
rs9366972	0.88[CEU][hapmap]
rs9366980	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369070	0.88[CEU][hapmap]
rs9369072	0.88[CEU][hapmap]
rs9369074	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs9369101	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369106	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380764	0.88[CEU][hapmap]
rs9380837	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394517	0.88[CEU][hapmap]
rs9394520	0.88[CEU][hapmap]
rs9394526	1.00[CEU][hapmap]
rs9394540	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][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	nsv830586	chr6:12130076-12295334	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12122200-12161800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:12137000-12163600	Weak transcription	Small Intestine	intestine
3	chr6:12139000-12161600	Weak transcription	HepG2	liver
4	chr6:12140200-12161800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:12140600-12161400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:12140600-12161400	Weak transcription	Pancreas	Pancrea
7	chr6:12140600-12161400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:12140600-12161400	Weak transcription	Spleen	Spleen
9	chr6:12140600-12161600	Weak transcription	Esophagus	oesophagus
10	chr6:12140600-12161800	Weak transcription	Gastric	stomach
11	chr6:12140600-12163600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:12140600-12163600	Weak transcription	Psoas Muscle	Psoas
13	chr6:12140600-12163800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:12140800-12160600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:12140800-12161000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:12140800-12161400	Weak transcription	Thymus	Thymus
17	chr6:12140800-12161600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:12140800-12161600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:12140800-12161800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:12140800-12161800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:12140800-12161800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:12140800-12162800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:12141000-12161600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:12141000-12161600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:12141000-12161800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:12141200-12162400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:12141800-12161600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:12148000-12161800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:12148800-12161400	Weak transcription	Left Ventricle	heart
30	chr6:12149400-12160600	Weak transcription	Fetal Thymus	thymus
31	chr6:12149400-12161000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:12149400-12161800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:12149400-12163600	Weak transcription	HMEC	breast
34	chr6:12149600-12161800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:12150200-12160600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:12150200-12160800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:12150200-12161400	Weak transcription	Ovary	ovary
38	chr6:12150200-12161600	Weak transcription	Brain Germinal Matrix	brain
39	chr6:12150200-12161800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:12150400-12165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:12150600-12160600	Weak transcription	NH-A	brain
42	chr6:12150600-12163200	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:12150600-12163400	Weak transcription	Fetal Brain Female	brain
44	chr6:12150600-12166800	Weak transcription	Fetal Brain Male	brain
45	chr6:12151600-12161800	Weak transcription	NHEK	skin
46	chr6:12151800-12160600	Weak transcription	Fetal Intestine Large	intestine
47	chr6:12152000-12160600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:12152000-12161600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:12152000-12166600	Weak transcription	Fetal Heart	heart
50	chr6:12152200-12166000	Weak transcription	Stomach Mucosa	stomach

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