Variant report

Variant	rs6904975
Chromosome Location	chr6:28952035-28952036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:28952018-28952330	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28948706..28953416-chr6:28959003..28967079,12	K562	blood:
2	chr6:28946686..28952098-chr6:28981757..28987491,9	K562	blood:
3	chr6:28931535..28933777-chr6:28950543..28952333,2	K562	blood:
4	chr6:28677880..28679993-chr6:28950394..28952978,2	K562	blood:
5	chr6:28907253..28915101-chr6:28945522..28952393,17	K562	blood:
6	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
7	chr6:28858185..28860648-chr6:28949293..28952393,3	K562	blood:
8	chr6:28687246..28689887-chr6:28948960..28952398,3	K562	blood:
9	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
10	chr6:28805369..28807414-chr6:28949591..28952908,4	K562	blood:
11	chr6:28890052..28891752-chr6:28950586..28953290,2	MCF-7	breast:
12	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
13	chr6:28694799..28697435-chr6:28950609..28952532,2	K562	blood:
14	chr6:28889573..28894329-chr6:28949030..28952998,8	K562	blood:
15	chr6:28889725..28893274-chr6:28947221..28952049,9	MCF-7	breast:
16	chr6:28948241..28954799-chr6:28970209..28976187,12	MCF-7	breast:
17	chr6:28949395..28952854-chr6:28970269..28975682,5	K562	blood:
18	chr6:28888560..28894615-chr6:28945306..28952099,20	K562	blood:

No data

Variant related genes	Relation type
HCG15	TF binding region
HCG16	TF binding region
ENSG00000225173	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1005123	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1237485	0.85[ASN][1000 genomes]
rs1476016	0.91[ASN][1000 genomes]
rs1543796	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1794587	0.84[ASN][1000 genomes]
rs184093	0.84[ASN][1000 genomes]
rs2013848	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2032500	0.82[ASN][1000 genomes]
rs2071785	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071790	0.89[ASN][1000 genomes]
rs209122	0.85[ASN][1000 genomes]
rs209126	0.85[ASN][1000 genomes]
rs209128	0.84[ASN][1000 genomes]
rs209129	0.84[ASN][1000 genomes]
rs209137	0.82[ASN][1000 genomes]
rs209148	0.83[ASN][1000 genomes]
rs209149	0.82[ASN][1000 genomes]
rs2157312	0.90[ASN][1000 genomes]
rs2157313	0.90[ASN][1000 genomes]
rs2179648	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2187807	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2187808	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2269555	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2394512	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2765229	0.84[ASN][1000 genomes]
rs3129097	0.83[AMR][1000 genomes]
rs3129792	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3129793	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3130775	0.82[AMR][1000 genomes]
rs3130841	0.85[ASN][1000 genomes]
rs3130842	0.90[ASN][1000 genomes]
rs3130886	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3130889	0.90[ASN][1000 genomes]
rs3130897	0.88[ASN][1000 genomes]
rs3131070	0.90[ASN][1000 genomes]
rs3131074	0.90[ASN][1000 genomes]
rs3131077	0.90[ASN][1000 genomes]
rs3135319	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3135321	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3135322	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3135323	0.91[ASN][1000 genomes]
rs3135324	0.91[ASN][1000 genomes]
rs3135327	0.82[ASN][1000 genomes]
rs3135328	0.90[ASN][1000 genomes]
rs381808	0.83[ASN][1000 genomes]
rs4427026	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713186	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713187	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713188	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713190	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713192	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4947339	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456876	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456880	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456883	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6456891	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900967	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6901599	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906909	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914955	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916161	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920392	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6927132	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6931823	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763009	0.90[ASN][1000 genomes]
rs7743189	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7761547	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7768299	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9257401	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9257404	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257405	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257408	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9257421	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257447	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257449	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257455	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257461	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9257464	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9348816	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348817	0.88[AMR][1000 genomes]
rs9380109	0.84[AMR][1000 genomes]
rs9393939	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393942	0.82[AMR][1000 genomes]
rs9468467	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468472	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468480	0.82[AMR][1000 genomes];0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6904975	ZNF323	cis	cerebellum	SCAN
rs6904975	ZSCAN16	cis	parietal	SCAN
rs6904975	HIST1H2AE	cis	parietal	SCAN
rs6904975	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28948600-28954800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:28950000-28952400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:28950000-28952800	Weak transcription	Small Intestine	intestine
4	chr6:28950000-28953400	Weak transcription	Lung	lung
5	chr6:28950000-28953600	Weak transcription	Spleen	Spleen
6	chr6:28950400-28953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:28950600-28952200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:28950600-28952400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:28950600-28952400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:28950600-28952400	Weak transcription	Colonic Mucosa	Colon
11	chr6:28950600-28952600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:28950600-28952600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28950600-28952600	Weak transcription	Left Ventricle	heart
14	chr6:28950600-28952600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:28950600-28952600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:28950600-28952800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:28950600-28952800	Weak transcription	Stomach Mucosa	stomach
18	chr6:28950600-28953200	Weak transcription	Esophagus	oesophagus
19	chr6:28950600-28953200	Weak transcription	Pancreas	Pancrea
20	chr6:28950800-28952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:28950800-28952200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:28950800-28952200	Weak transcription	Brain Germinal Matrix	brain
23	chr6:28950800-28952200	Weak transcription	Right Atrium	heart
24	chr6:28950800-28952200	Weak transcription	Right Ventricle	heart
25	chr6:28950800-28952400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:28950800-28952400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:28950800-28952400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:28950800-28952600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:28950800-28952600	Weak transcription	Aorta	Aorta
30	chr6:28950800-28952800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:28950800-28952800	Weak transcription	Placenta	Placenta
32	chr6:28950800-28952800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:28950800-28953000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:28950800-28953000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:28950800-28953000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:28950800-28954200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:28951000-28952200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:28951000-28952200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:28951000-28952200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:28951000-28952200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:28951000-28952200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:28951000-28952200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:28951000-28952200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:28951000-28952200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:28951000-28952200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:28951000-28952200	Weak transcription	Fetal Brain Female	brain
47	chr6:28951000-28952200	Weak transcription	Fetal Kidney	kidney
48	chr6:28951000-28952200	Weak transcription	Fetal Lung	lung
49	chr6:28951000-28952200	Weak transcription	Ovary	ovary
50	chr6:28951000-28952200	Weak transcription	HUVEC	blood vessel

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