Variant report

Variant	rs1039302
Chromosome Location	chr12:121236258-121236259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121223533..121225993-chr12:121234568..121236764,2	K562	blood:
2	chr12:121226286..121228196-chr12:121235174..121237034,2	K562	blood:
3	chr12:121230474..121232207-chr12:121234744..121236452,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1027556	1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10431387	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10437838	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10744754	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10774568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774569	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10774571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10849782	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10849786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849787	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10849788	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10849790	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10849793	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10849800	0.84[ASN][1000 genomes]
rs10849810	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10849811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10849814	0.82[GIH][hapmap]
rs11065259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065272	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065298	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11065322	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs1151849	0.86[YRI][hapmap]
rs1151862	0.86[YRI][hapmap]
rs11829904	0.81[YRI][hapmap]
rs11833706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13746	0.83[YRI][hapmap]
rs2393718	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2393725	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213568	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3213569	0.84[GIH][hapmap]
rs3213571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3809314	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs4638383	0.83[AFR][1000 genomes]
rs471688	0.86[YRI][hapmap]
rs508595	0.80[YRI][hapmap]
rs531782	0.93[YRI][hapmap]
rs593429	0.85[ASN][1000 genomes]
rs610694	0.86[YRI][hapmap]
rs624216	0.86[YRI][hapmap]
rs625228	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs6489780	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]
rs6489781	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6489782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661647	0.80[YRI][hapmap]
rs7135147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7135426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs715319	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7298639	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7300695	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73229114	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7960784	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7977343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Quantitative traits	19197348	GWAS catalog

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
2	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:121211400-121260800	Weak transcription	Gastric	stomach
4	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
5	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:121221400-121240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:121221600-121238800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:121222200-121237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:121222200-121274000	Weak transcription	Lung	lung
11	chr12:121222400-121238800	Weak transcription	Placenta	Placenta
12	chr12:121222400-121240400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:121222600-121237200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:121222600-121249200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:121222600-121259000	Weak transcription	Ovary	ovary
16	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
17	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
18	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:121222800-121237200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:121222800-121237400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:121222800-121240600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:121222800-121245600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:121222800-121249400	Weak transcription	HSMM	muscle
24	chr12:121226200-121237200	Weak transcription	Psoas Muscle	Psoas
25	chr12:121228600-121239400	Weak transcription	Liver	Liver
26	chr12:121229000-121245200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:121230000-121239000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:121230000-121255200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:121231200-121238000	Weak transcription	Left Ventricle	heart
30	chr12:121231600-121237400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:121233600-121237000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:121234000-121236600	Weak transcription	NHEK	skin
33	chr12:121234000-121237000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:121234000-121240200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:121234000-121240600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:121234000-121240800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:121234200-121246000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:121234200-121246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:121234200-121246600	Weak transcription	Fetal Stomach	stomach
41	chr12:121234200-121246800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:121234600-121236800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:121234600-121238600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:121234600-121238600	Weak transcription	Fetal Lung	lung
45	chr12:121234600-121239000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:121234600-121245800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:121234600-121246000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:121234600-121247200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:121234600-121250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:121234600-121263000	Weak transcription	A549	lung

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