Variant report

Variant	rs209128
Chromosome Location	chr6:28869173-28869174
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28864301..28866368-chr6:28868615..28871071,3	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
4	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
5	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1002925	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1005123	0.83[ASN][1000 genomes]
rs1233602	0.81[EUR][1000 genomes]
rs1237485	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476016	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543796	0.82[ASN][1000 genomes]
rs169683	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1794587	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184093	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013848	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2032500	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2071785	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2071790	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209122	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209126	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs209129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209148	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209149	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209152	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs209153	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209160	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209161	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209163	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209164	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209169	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs209171	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209173	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209175	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209176	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209179	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209182	0.84[EUR][1000 genomes]
rs209184	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209186	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2157312	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2157313	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2179648	0.80[ASN][1000 genomes]
rs2187807	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2187808	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2208536	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2269555	0.84[ASN][1000 genomes]
rs2394512	0.82[ASN][1000 genomes]
rs2754764	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754767	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2765218	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2765219	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2765229	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129792	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129793	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130841	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130842	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130886	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130889	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130897	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131070	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131074	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131077	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131099	0.83[AMR][1000 genomes]
rs3131100	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131102	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131342	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3132371	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3132386	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135303	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3135319	0.82[EUR][1000 genomes]
rs3135321	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135322	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135323	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135324	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135326	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135327	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3135328	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs377392	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs381808	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs386628	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs393431	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4427026	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4713186	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4713187	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4713188	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4713190	0.86[ASN][1000 genomes]
rs4713192	0.86[ASN][1000 genomes]
rs4947339	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs526983	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456857	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6456876	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6456880	0.85[ASN][1000 genomes]
rs6456883	0.84[ASN][1000 genomes]
rs6901599	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6904975	0.84[ASN][1000 genomes]
rs6906909	0.84[ASN][1000 genomes]
rs6914955	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6916161	0.84[ASN][1000 genomes]
rs6920392	0.86[ASN][1000 genomes]
rs6931823	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs763009	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7743189	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7755875	0.89[ASN][1000 genomes]
rs7761547	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7768299	0.82[ASN][1000 genomes]
rs9257401	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9257404	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9257405	0.89[ASN][1000 genomes]
rs9257408	0.82[ASN][1000 genomes]
rs9257421	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9257447	0.85[ASN][1000 genomes]
rs9257449	0.85[ASN][1000 genomes]
rs9257455	0.82[ASN][1000 genomes]
rs9257461	0.84[ASN][1000 genomes]
rs9348816	0.82[ASN][1000 genomes]
rs9393939	0.82[ASN][1000 genomes]
rs9468467	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs209128	HIST1H2BH	cis	cerebellum	SCAN
rs209128	ZSCAN23	cis	cerebellum	SCAN
rs209128	NKAPL	cis	parietal	SCAN
rs209128	ZSCAN23	cis	parietal	SCAN
rs209128	ZNF323	cis	cerebellum	SCAN
rs209128	ZSCAN16	cis	parietal	SCAN
rs209128	ZKSCAN3	cis	cerebellum	SCAN
rs209128	ZNF323	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28865000-28869200	Weak transcription	Gastric	stomach
2	chr6:28865000-28870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:28865000-28870600	Weak transcription	Stomach Mucosa	stomach
4	chr6:28865000-28870800	Weak transcription	Small Intestine	intestine
5	chr6:28865200-28869200	Weak transcription	Esophagus	oesophagus
6	chr6:28865200-28869200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:28865200-28870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:28865200-28871400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:28865200-28878200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:28865400-28869600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:28865400-28870600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:28865400-28870600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:28865600-28870400	Weak transcription	Brain Substantia Nigra	brain
14	chr6:28865600-28870800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:28865600-28871600	Weak transcription	Fetal Heart	heart
16	chr6:28865800-28869200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:28866000-28869400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:28866000-28870400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:28866000-28870400	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:28866000-28870600	Weak transcription	Right Ventricle	heart
21	chr6:28866000-28870800	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:28866000-28871600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:28866200-28869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:28866200-28869400	Weak transcription	Ovary	ovary
26	chr6:28866200-28869600	Weak transcription	Fetal Stomach	stomach
27	chr6:28866200-28870200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:28866200-28870600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:28866200-28874200	Weak transcription	Right Atrium	heart
30	chr6:28866400-28869200	Weak transcription	NHDF-Ad	bronchial
31	chr6:28866400-28869400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:28866400-28870800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:28867000-28889400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:28867600-28889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:28867600-28889400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:28867600-28889600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:28867800-28869400	Strong transcription	K562	blood
38	chr6:28867800-28873200	Strong transcription	A549	lung
39	chr6:28867800-28874200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:28867800-28874600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:28867800-28874600	Strong transcription	NH-A	brain
42	chr6:28867800-28874600	Strong transcription	Osteobl	bone
43	chr6:28867800-28878800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:28867800-28880000	Strong transcription	Primary T cells from cord blood	blood
45	chr6:28867800-28881600	Strong transcription	HSMM	muscle
46	chr6:28867800-28883200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr6:28867800-28885400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:28867800-28888200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:28867800-28888400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:28867800-28888400	Strong transcription	Fetal Thymus	thymus

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