Variant report

Variant	rs12600271
Chromosome Location	chr16:75633618-75633619
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	chr16:75633557..75635461-chr16:75635525..75638161,2	MCF-7	breast:
2	chr16:75627208..75629939-chr16:75629940..75634197,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10871314	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11149842	0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12443899	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12445389	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12445937	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12446652	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12595883	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12596033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12596083	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12596724	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12596857	0.80[AMR][1000 genomes]
rs12598094	0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12598741	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12598751	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12599212	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12599322	0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12600066	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16940253	0.87[JPT][hapmap];0.95[AMR][1000 genomes]
rs16940467	0.85[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17697211	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17764821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17764918	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1812507	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1836547	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1865493	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1979717	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2059261	0.83[AMR][1000 genomes]
rs2082751	0.85[ASN][1000 genomes]
rs2164245	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242406	1.00[CEU][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278469	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2903096	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35977374	0.82[AMR][1000 genomes]
rs3736377	0.90[AMR][1000 genomes]
rs3743599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743601	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3743603	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743605	0.94[AMR][1000 genomes]
rs3784929	0.87[JPT][hapmap]
rs3826108	0.84[AMR][1000 genomes]
rs3851741	0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41505349	0.87[JPT][hapmap]
rs4482320	0.85[AMR][1000 genomes]
rs4633754	0.82[AMR][1000 genomes]
rs4887833	0.91[AMR][1000 genomes]
rs4887835	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4887836	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4887837	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4888437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4888440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4888442	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888444	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4888448	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4888449	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888451	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888455	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5010692	0.87[JPT][hapmap]
rs56954102	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57208266	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57252551	0.95[AMR][1000 genomes]
rs57396453	0.85[ASN][1000 genomes]
rs58091977	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58264015	0.83[AMR][1000 genomes]
rs58273293	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58508930	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58533792	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58597869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58673511	0.90[AMR][1000 genomes]
rs58719566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58846463	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59449831	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59907199	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60393074	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60952428	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61036571	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61078946	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61164110	0.81[AMR][1000 genomes]
rs61183686	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61537885	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61539645	0.86[AMR][1000 genomes]
rs6564268	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7187419	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7187672	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7193066	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7195338	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs719574	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206799	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74027438	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7499759	0.99[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8048533	0.82[AMR][1000 genomes]
rs8051713	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8053219	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs8055329	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8056968	0.99[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8060972	0.88[JPT][hapmap];0.86[AMR][1000 genomes]
rs8192516	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963820	0.94[JPT][hapmap];0.87[AMR][1000 genomes]
rs9788802	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9934159	0.87[JPT][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
8	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75610400-75634000	Weak transcription	Hela-S3	cervix
2	chr16:75610600-75635200	Weak transcription	Fetal Kidney	kidney
3	chr16:75611400-75634000	Weak transcription	Colonic Mucosa	Colon
4	chr16:75612000-75635600	Weak transcription	Small Intestine	intestine
5	chr16:75613400-75635200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:75625400-75635400	Weak transcription	Brain Substantia Nigra	brain
7	chr16:75625600-75648000	Weak transcription	Fetal Heart	heart
8	chr16:75628000-75635200	Weak transcription	Right Ventricle	heart
9	chr16:75628200-75634000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:75628600-75635000	Weak transcription	NHLF	lung
11	chr16:75628600-75635800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:75628600-75636600	Weak transcription	Stomach Mucosa	stomach
13	chr16:75628800-75634000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr16:75629000-75635200	Weak transcription	K562	blood
15	chr16:75629000-75636000	Weak transcription	NHDF-Ad	bronchial
16	chr16:75629000-75650600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr16:75629400-75635200	Weak transcription	HUVEC	blood vessel
18	chr16:75629400-75635800	Strong transcription	Primary T cells from cord blood	blood
19	chr16:75629400-75635800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr16:75629400-75636000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:75629600-75635800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr16:75629600-75636200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr16:75629600-75654800	Strong transcription	Fetal Stomach	stomach
24	chr16:75629800-75636000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr16:75630200-75636000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr16:75630200-75636000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:75630200-75636000	Strong transcription	Dnd41	blood
28	chr16:75630200-75638200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:75630600-75654600	Strong transcription	Fetal Intestine Large	intestine
30	chr16:75630800-75635800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr16:75630800-75635800	Strong transcription	GM12878-XiMat	blood
32	chr16:75630800-75636000	Strong transcription	Placenta	Placenta
33	chr16:75630800-75636200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:75630800-75636400	Strong transcription	Fetal Brain Female	brain
35	chr16:75630800-75638000	Strong transcription	Adipose Nuclei	Adipose
36	chr16:75631000-75635800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr16:75631000-75636000	Weak transcription	Fetal Brain Male	brain
38	chr16:75631000-75636200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr16:75631000-75636200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr16:75631000-75638000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr16:75631000-75638000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr16:75631000-75638200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr16:75631000-75649400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr16:75631200-75637400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr16:75631400-75634000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr16:75631400-75634000	Weak transcription	Aorta	Aorta
47	chr16:75631400-75634600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr16:75631400-75635600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr16:75631400-75635800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:75631400-75636000	Strong transcription	Fetal Intestine Small	intestine

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