Variant report

Variant	rs1916572
Chromosome Location	chr10:52169371-52169372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52169351..52171614-chr10:52383137..52385648,2	K562	blood:
2	chr10:52164829..52166437-chr10:52168704..52170422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10458673	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10508927	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10508928	0.89[CEU][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10508929	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10740684	0.98[ASN][1000 genomes]
rs10763365	0.85[EUR][1000 genomes]
rs10763373	0.90[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10763382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10763392	0.84[JPT][hapmap]
rs10763426	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10763500	0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10763535	0.83[CEU][hapmap]
rs10825789	0.90[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10825825	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10825859	0.94[ASN][1000 genomes]
rs10825861	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10825882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10825904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10825934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10825978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10825995	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10825996	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10826013	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10826033	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10826036	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10826169	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11005213	1.00[YRI][hapmap]
rs11005241	1.00[YRI][hapmap]
rs11005262	1.00[YRI][hapmap]
rs11005278	1.00[YRI][hapmap]
rs11005356	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11005399	0.90[CEU][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11005415	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11005418	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11005579	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11005621	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11005761	0.89[ASN][1000 genomes]
rs11005803	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11005884	0.87[ASN][1000 genomes]
rs11006054	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs11006075	0.81[AMR][1000 genomes]
rs12217518	1.00[YRI][hapmap]
rs12217648	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12219070	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12219692	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1884572	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024872	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2144863	0.84[ASN][1000 genomes]
rs2273402	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2339400	0.83[JPT][hapmap]
rs2339401	0.84[JPT][hapmap]
rs2339503	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2339507	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs34122137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739989	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4519042	0.81[AFR][1000 genomes]
rs4935165	0.87[ASN][1000 genomes]
rs4935711	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4935728	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7079881	0.84[ASN][1000 genomes]
rs7086029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089882	1.00[YRI][hapmap]
rs7090807	0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7092749	0.89[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7096171	1.00[YRI][hapmap]
rs768185	0.89[CEU][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7896315	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7904375	0.87[EUR][1000 genomes]
rs7908163	0.83[EUR][1000 genomes]
rs7920818	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7922802	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs910817	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs927047	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs927048	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9919413	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52142600-52170200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:52156200-52170200	Weak transcription	Pancreas	Pancrea
4	chr10:52157000-52170800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr10:52157200-52170000	Weak transcription	Gastric	stomach
6	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
7	chr10:52157400-52170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:52157800-52172000	Weak transcription	Fetal Lung	lung
9	chr10:52157800-52173200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr10:52157800-52176800	Weak transcription	Lung	lung
12	chr10:52158800-52169400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr10:52158800-52172200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr10:52163200-52170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:52163400-52170000	Weak transcription	NHLF	lung
17	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
18	chr10:52164400-52170000	Weak transcription	Brain Substantia Nigra	brain
19	chr10:52164400-52170000	Enhancers	Hela-S3	cervix
20	chr10:52164400-52170200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr10:52164400-52172400	Weak transcription	Ovary	ovary
22	chr10:52164400-52173800	Weak transcription	Psoas Muscle	Psoas
23	chr10:52164400-52174000	Weak transcription	Brain Angular Gyrus	brain
24	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:52164600-52171000	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr10:52165200-52171600	Weak transcription	Brain Anterior Caudate	brain
28	chr10:52165400-52171800	Weak transcription	Liver	Liver
29	chr10:52166200-52169800	Weak transcription	Esophagus	oesophagus
30	chr10:52166200-52170000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:52166400-52170000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:52166400-52170000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr10:52166400-52170200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:52166400-52170200	Genic enhancers	K562	blood
35	chr10:52166600-52170400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
37	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr10:52166800-52171400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:52167000-52170000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:52167600-52170000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr10:52167600-52173000	Weak transcription	HepG2	liver
48	chr10:52167600-52176800	Weak transcription	Primary B cells from cord blood	blood
49	chr10:52167800-52171400	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr10:52168000-52169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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