Variant report

Variant	rs974459
Chromosome Location	chr12:59991492-59991493
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	chr12:59990876..59991528-chr9:32552220..32553126,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000197579	Chromatin interaction
ENSG00000235453	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506395	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732745	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735880	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735881	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747847	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10747848	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10747850	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747851	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747852	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783988	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783989	0.85[EUR][1000 genomes]
rs10783992	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877315	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877320	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173084	0.85[EUR][1000 genomes]
rs11173085	0.82[EUR][1000 genomes]
rs11173087	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11173090	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391130	0.81[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497470	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566164	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908977	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1966281	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2132871	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2132873	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646311	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2671854	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3106580	0.84[EUR][1000 genomes]
rs35986083	0.86[EUR][1000 genomes]
rs4019983	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4421780	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4536269	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635118	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4760291	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760292	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760293	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760294	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581255	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6581256	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6581257	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581258	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581259	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581260	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581261	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133515	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133612	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303302	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312134	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970605	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975216	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59988800-59991600	Active TSS	Duodenum Mucosa	Duodenum
2	chr12:59988800-59991800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:59989000-59991600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:59989000-59991600	Active TSS	Brain Germinal Matrix	brain
5	chr12:59989000-59991600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr12:59989000-59992000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr12:59989200-59991600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:59989200-59991600	Active TSS	GM12878-XiMat	blood
9	chr12:59989200-59991800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:59989200-59991800	Active TSS	NHDF-Ad	bronchial
11	chr12:59989200-59992000	Active TSS	Aorta	Aorta
12	chr12:59989200-59992000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:59989200-59992000	Active TSS	Right Atrium	heart
14	chr12:59989400-59991600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:59989400-59991600	Active TSS	Rectal Smooth Muscle	rectum
16	chr12:59989600-59991600	Active TSS	Brain Hippocampus Middle	brain
17	chr12:59990000-59991600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:59990200-59991800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:59990200-59992000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:59990400-59991600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr12:59990600-59991600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:59990600-59991600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr12:59990800-59991600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:59990800-59992000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:59990800-59992000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr12:59990800-59992200	Flanking Active TSS	Fetal Heart	heart
27	chr12:59991000-59991600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr12:59991000-59991600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr12:59991000-59991600	Flanking Active TSS	NHLF	lung
30	chr12:59991000-59991800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr12:59991000-59991800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr12:59991000-59991800	Flanking Active TSS	Dnd41	blood
33	chr12:59991000-60005000	Weak transcription	Lung	lung
34	chr12:59991200-59991600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr12:59991200-59991600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr12:59991200-59991600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:59991200-59991600	Active TSS	Stomach Smooth Muscle	stomach
38	chr12:59991200-59991800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:59991200-60004600	Weak transcription	Ovary	ovary
40	chr12:59991400-59991600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr12:59991400-59991600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:59991400-59991600	Enhancers	Primary B cells from peripheral blood	blood
43	chr12:59991400-59991600	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:59991400-59991600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:59991400-59991600	Enhancers	Brain Angular Gyrus	brain
46	chr12:59991400-59991600	Enhancers	Brain Anterior Caudate	brain
47	chr12:59991400-59991600	Enhancers	Brain Cingulate Gyrus	brain
48	chr12:59991400-59991600	Active TSS	Fetal Muscle Leg	muscle
49	chr12:59991400-59991600	Enhancers	Fetal Stomach	stomach
50	chr12:59991400-59991600	Active TSS	Fetal Thymus	thymus

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