Variant report

Variant	rs10130959
Chromosome Location	chr14:39741964-39741965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:39741845-39741988	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39736982..39739247-chr14:39739513..39742286,3	K562	blood:
2	chr14:39734713..39738415-chr14:39740999..39745819,7	MCF-7	breast:
3	chr14:39733456..39736427-chr14:39738159..39742075,4	K562	blood:
4	chr14:39733186..39738068-chr14:39738751..39742738,6	MCF-7	breast:

Variant related genes	Relation type
CTAGE5	TF binding region
ENSG00000150527	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000258940	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10142118	0.81[ASN][1000 genomes]
rs10143290	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs10144680	0.81[ASN][1000 genomes]
rs10148678	0.81[ASN][1000 genomes]
rs10148762	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs10150863	0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs1040811	0.89[ASN][1000 genomes]
rs10483539	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs10782392	0.89[ASN][1000 genomes]
rs10872919	0.89[ASN][1000 genomes]
rs11157055	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11844333	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11844337	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12434446	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs2025029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2038357	0.93[TSI][hapmap]
rs2094275	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2099409	0.89[ASN][1000 genomes]
rs2415548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3783292	0.82[CEU][hapmap]
rs4899219	1.00[JPT][hapmap]
rs4899237	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4902402	0.93[TSI][hapmap]
rs4902500	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs6571914	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6571916	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6571917	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs6571934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7140427	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7140561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7143289	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7149131	1.00[JPT][hapmap]
rs7151017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7158558	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158633	0.81[ASN][1000 genomes]
rs7159584	0.81[ASN][1000 genomes]
rs8010635	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8010826	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8011855	0.93[TSI][hapmap]
rs8019161	0.82[CEU][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap]
rs9322993	0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39737000-39751800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:39737800-39748800	Weak transcription	Right Ventricle	heart
3	chr14:39737800-39750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:39737800-39763800	Weak transcription	Gastric	stomach
5	chr14:39738000-39742400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr14:39738000-39742600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr14:39738000-39744400	Weak transcription	Right Atrium	heart
8	chr14:39738000-39748800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:39738000-39750600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:39738000-39752000	Weak transcription	Stomach Mucosa	stomach
11	chr14:39738000-39763800	Weak transcription	HSMM	muscle
12	chr14:39738200-39742000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr14:39738200-39745000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:39738200-39747000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr14:39738200-39748800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr14:39738200-39748800	Weak transcription	Fetal Kidney	kidney
17	chr14:39738200-39748800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr14:39738200-39748800	Weak transcription	Osteobl	bone
19	chr14:39738200-39751800	Weak transcription	Colonic Mucosa	Colon
20	chr14:39738200-39751800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:39738200-39759200	Weak transcription	NH-A	brain
22	chr14:39738200-39763800	Weak transcription	Brain Angular Gyrus	brain
23	chr14:39738200-39763800	Weak transcription	HSMMtube	muscle
24	chr14:39738200-39766200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:39738200-39813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:39738600-39763800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr14:39738800-39747800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr14:39738800-39748800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr14:39738800-39748800	Weak transcription	Adipose Nuclei	Adipose
30	chr14:39738800-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr14:39738800-39748800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr14:39738800-39764800	Weak transcription	NHDF-Ad	bronchial
33	chr14:39739000-39746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:39739000-39747200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr14:39739000-39748800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:39739000-39751800	Weak transcription	Brain Anterior Caudate	brain
37	chr14:39739200-39743800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr14:39739200-39747600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr14:39739200-39748800	Weak transcription	Brain Hippocampus Middle	brain
40	chr14:39739200-39748800	Weak transcription	HUVEC	blood vessel
41	chr14:39739200-39764000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr14:39739400-39745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:39739400-39746400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr14:39739400-39747200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr14:39739400-39748800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr14:39739400-39749200	Weak transcription	Small Intestine	intestine
47	chr14:39739400-39758200	Weak transcription	NHEK	skin
48	chr14:39739800-39747000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:39739800-39763400	Weak transcription	Lung	lung
50	chr14:39739800-39766400	Weak transcription	Aorta	Aorta

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