Variant report

Variant	rs6489780
Chromosome Location	chr12:121228410-121228411
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121224775..121227076-chr12:121227465..121229261,2	K562	blood:
2	chr12:121227665..121229362-chr12:121229925..121232592,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1027556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1039302	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10431387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10437838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744754	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10774569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10774570	1.00[CEU][hapmap]
rs10774571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10849782	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10849785	0.92[MEX][hapmap]
rs10849786	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10849787	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849789	0.92[MEX][hapmap]
rs10849790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849792	0.92[MEX][hapmap]
rs10849793	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10849794	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10849800	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10849805	0.86[CEU][hapmap]
rs10849808	0.92[MEX][hapmap]
rs10849810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10849811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10849814	1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap]
rs11065259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11065266	0.94[EUR][1000 genomes]
rs11065272	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11065298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11065322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1151849	0.86[YRI][hapmap]
rs1151862	0.86[YRI][hapmap]
rs11829904	0.81[YRI][hapmap]
rs11833706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423697	0.83[EUR][1000 genomes]
rs13746	0.83[YRI][hapmap]
rs2393718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2393725	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3213568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213569	1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.94[EUR][1000 genomes]
rs3213571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4638383	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs471688	0.86[YRI][hapmap]
rs508595	0.80[YRI][hapmap]
rs531782	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs56137011	0.83[EUR][1000 genomes]
rs593429	0.83[ASN][1000 genomes]
rs610694	0.86[YRI][hapmap]
rs624216	0.86[YRI][hapmap]
rs625228	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs6489781	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6489782	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6490303	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7135147	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7135426	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7139145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs715319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7298639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7300695	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73229114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960784	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7965332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7977343	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1801139	chr12:121228410-121241933	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
2	chr12:121207200-121233000	Weak transcription	HSMMtube	muscle
3	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:121211400-121260800	Weak transcription	Gastric	stomach
5	chr12:121212600-121229600	Weak transcription	Right Atrium	heart
6	chr12:121212600-121229800	Weak transcription	Right Ventricle	heart
7	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
8	chr12:121213200-121231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:121221200-121229600	Weak transcription	Osteobl	bone
11	chr12:121221200-121233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:121221200-121233600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:121221400-121229800	Weak transcription	NHDF-Ad	bronchial
15	chr12:121221400-121230400	Weak transcription	HMEC	breast
16	chr12:121221400-121231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:121221400-121232800	Weak transcription	A549	lung
18	chr12:121221400-121235800	Weak transcription	Hela-S3	cervix
19	chr12:121221400-121240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:121221600-121238800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:121222000-121229400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:121222000-121233200	Weak transcription	NHEK	skin
23	chr12:121222000-121233800	Weak transcription	Fetal Stomach	stomach
24	chr12:121222200-121229400	Weak transcription	HepG2	liver
25	chr12:121222200-121230200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:121222200-121231200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:121222200-121231200	Weak transcription	Fetal Brain Female	brain
28	chr12:121222200-121237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:121222200-121274000	Weak transcription	Lung	lung
30	chr12:121222400-121229600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:121222400-121231200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:121222400-121238800	Weak transcription	Placenta	Placenta
33	chr12:121222400-121240400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:121222600-121229400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:121222600-121229600	Weak transcription	Colonic Mucosa	Colon
36	chr12:121222600-121229600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:121222600-121229800	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:121222600-121230600	Weak transcription	Adipose Nuclei	Adipose
39	chr12:121222600-121231000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:121222600-121231200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:121222600-121232200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:121222600-121233200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:121222600-121237200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:121222600-121249200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:121222600-121259000	Weak transcription	Ovary	ovary
46	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
47	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
48	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:121222800-121228800	Weak transcription	Fetal Intestine Large	intestine
50	chr12:121222800-121229200	Weak transcription	Rectal Mucosa Donor 29	rectum

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