Variant report

Variant	rs3135322
Chromosome Location	chr6:28946920-28946921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28889158..28893048-chr6:28945668..28948691,6	K562	blood:
2	chr6:28946686..28952098-chr6:28981757..28987491,9	K562	blood:
3	chr6:28853392..28856962-chr6:28946124..28948045,3	K562	blood:
4	chr6:28829291..28833354-chr6:28946684..28949723,4	K562	blood:
5	chr6:28890727..28894097-chr6:28943047..28947323,5	MCF-7	breast:
6	chr6:28907253..28915101-chr6:28945522..28952393,17	K562	blood:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
8	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
9	chr6:28888560..28894615-chr6:28945306..28952099,20	K562	blood:
10	chr6:28940964..28943621-chr6:28945663..28948952,4	K562	blood:
11	chr6:27859640..27862411-chr6:28946747..28949086,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1002925	0.85[EUR][1000 genomes]
rs1005123	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1237485	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1476016	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543796	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169683	0.84[EUR][1000 genomes]
rs1794587	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184093	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2013848	0.92[ASN][1000 genomes]
rs2032500	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071785	0.91[ASN][1000 genomes]
rs2071790	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209122	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209126	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209128	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209129	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209137	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209138	0.88[EUR][1000 genomes]
rs209148	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209149	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs209152	0.84[EUR][1000 genomes]
rs209153	0.87[EUR][1000 genomes]
rs209160	0.85[EUR][1000 genomes]
rs209161	0.87[EUR][1000 genomes]
rs209163	0.87[EUR][1000 genomes]
rs209164	0.84[EUR][1000 genomes]
rs209171	0.81[EUR][1000 genomes]
rs209173	0.82[EUR][1000 genomes]
rs209175	0.81[EUR][1000 genomes]
rs209176	0.85[EUR][1000 genomes]
rs209179	0.82[EUR][1000 genomes]
rs209184	0.85[EUR][1000 genomes]
rs209186	0.84[EUR][1000 genomes]
rs2157312	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2157313	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179648	0.94[ASN][1000 genomes]
rs2187807	0.92[ASN][1000 genomes]
rs2187808	0.92[ASN][1000 genomes]
rs2206040	0.91[AFR][1000 genomes]
rs2206041	0.91[AFR][1000 genomes]
rs2208536	0.84[EUR][1000 genomes]
rs2269555	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2394512	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2754764	0.84[EUR][1000 genomes]
rs2754767	0.84[EUR][1000 genomes]
rs2765218	0.83[EUR][1000 genomes]
rs2765219	0.84[EUR][1000 genomes]
rs2765229	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3116844	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3129145	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3129150	0.82[AMR][1000 genomes]
rs3129792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129793	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130718	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3130841	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130842	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130886	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130889	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130897	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131070	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131074	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131077	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131100	0.80[EUR][1000 genomes]
rs3131102	0.91[EUR][1000 genomes]
rs3131342	0.84[EUR][1000 genomes]
rs3132371	0.80[EUR][1000 genomes]
rs3132386	0.85[EUR][1000 genomes]
rs3135303	0.87[EUR][1000 genomes]
rs3135315	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3135323	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135324	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135326	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135327	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3135328	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs377392	0.85[EUR][1000 genomes]
rs381808	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs386628	0.85[EUR][1000 genomes]
rs393431	0.85[EUR][1000 genomes]
rs4427026	0.92[ASN][1000 genomes]
rs4713186	0.89[ASN][1000 genomes]
rs4713187	0.89[ASN][1000 genomes]
rs4713188	0.90[ASN][1000 genomes]
rs4713190	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713192	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4947339	0.92[ASN][1000 genomes]
rs526983	0.82[EUR][1000 genomes]
rs6456876	0.92[ASN][1000 genomes]
rs6456880	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6456883	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6456891	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6900967	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6901599	0.92[ASN][1000 genomes]
rs6904975	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6906909	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6914955	0.91[ASN][1000 genomes]
rs6916161	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6920392	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6931823	0.92[ASN][1000 genomes]
rs763009	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7743189	0.91[ASN][1000 genomes]
rs7761547	0.92[ASN][1000 genomes]
rs7768299	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9257401	0.92[ASN][1000 genomes]
rs9257404	0.91[ASN][1000 genomes]
rs9257405	0.90[ASN][1000 genomes]
rs9257408	0.82[ASN][1000 genomes]
rs9257421	0.90[ASN][1000 genomes]
rs9257447	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9257449	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9257455	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9257461	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9257464	0.85[ASN][1000 genomes]
rs9348816	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9348817	0.80[AMR][1000 genomes]
rs9380109	0.83[AFR][1000 genomes]
rs9393939	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9468467	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9468472	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9468480	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3135322	ZKSCAN3	cis	cerebellum	SCAN
rs3135322	ZNF323	cis	parietal	SCAN
rs3135322	NKAPL	cis	parietal	SCAN
rs3135322	ZSCAN23	cis	cerebellum	SCAN
rs3135322	HIST1H2BH	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28945400-28948200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:28945400-28948200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:28945400-28948200	Enhancers	Hela-S3	cervix
4	chr6:28945400-28948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:28945600-28947600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:28945600-28947800	Weak transcription	Colonic Mucosa	Colon
7	chr6:28945600-28948000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:28945600-28948200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:28945600-28948200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:28945600-28948200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:28945600-28948200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:28945600-28948400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:28945600-28948400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:28945600-28948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:28945600-28948400	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:28945600-28948400	Weak transcription	Right Atrium	heart
17	chr6:28945600-28948400	Weak transcription	Right Ventricle	heart
18	chr6:28945600-28948600	Weak transcription	NHLF	lung
19	chr6:28945800-28947000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:28945800-28947600	Enhancers	HepG2	liver
21	chr6:28945800-28948200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:28945800-28948200	Weak transcription	Brain Angular Gyrus	brain
23	chr6:28945800-28948200	Weak transcription	Brain Anterior Caudate	brain
24	chr6:28945800-28948400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:28946000-28948000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:28946000-28948000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:28946000-28948400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:28946200-28947000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:28946200-28947000	Enhancers	NHEK	skin
30	chr6:28946200-28947200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:28946200-28947200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:28946200-28947400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:28946200-28947400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:28946200-28947600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:28946200-28947800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:28946200-28948000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:28946200-28948000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:28946200-28948000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:28946200-28948400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:28946200-28948400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:28946200-28948400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:28946200-28948400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:28946200-28948400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:28946200-28948400	Weak transcription	Placenta	Placenta
45	chr6:28946200-28948400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:28946400-28947200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr6:28946400-28948000	Weak transcription	HUVEC	blood vessel
48	chr6:28946400-28948400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:28946400-28948400	Weak transcription	HMEC	breast
50	chr6:28946400-28948400	Weak transcription	NHDF-Ad	bronchial

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