Variant report

Variant	rs943472
Chromosome Location	chr6:33738442-33738443
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33738202..33740373-chr6:34111521..34114051,2	K562	blood:
2	chr6:33733421..33736486-chr6:33736727..33739454,3	K562	blood:
3	chr6:33677151..33680603-chr6:33737180..33740397,3	MCF-7	breast:
4	chr6:33738171..33740892-chr6:33996773..33998948,2	K562	blood:
5	chr6:33733658..33736198-chr6:33737954..33739952,2	K562	blood:
6	chr6:33725418..33728218-chr6:33736581..33739360,2	MCF-7	breast:
7	chr6:33683560..33685755-chr6:33736435..33739209,2	MCF-7	breast:
8	chr6:33736224..33739190-chr6:33745201..33746852,2	MCF-7	breast:
9	chr6:33717026..33719225-chr6:33737928..33740540,2	MCF-7	breast:
10	chr6:33737959..33740435-chr6:34032927..34035702,2	K562	blood:
11	chr6:33734585..33738916-chr6:33755602..33758855,4	MCF-7	breast:
12	chr6:33698259..33701003-chr6:33736395..33738930,2	K562	blood:
13	chr6:33729337..33731009-chr6:33738048..33739817,2	MCF-7	breast:
14	chr6:33558047..33560338-chr6:33737884..33740577,2	K562	blood:
15	chr6:33734392..33738843-chr6:33747253..33751824,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124493	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10755683	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10947428	0.84[CEU][hapmap]
rs10947436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947446	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes]
rs11751943	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318691	0.87[EUR][1000 genomes]
rs1536500	0.89[EUR][1000 genomes]
rs1536501	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547668	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951930	0.83[AFR][1000 genomes]
rs1998949	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2182658	0.85[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2182659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395446	0.86[EUR][1000 genomes]
rs2395447	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395448	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2967	1.00[JPT][hapmap]
rs3957165	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4711350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713676	0.82[EUR][1000 genomes]
rs4713685	0.85[ASW][hapmap]
rs4713687	0.85[AFR][1000 genomes]
rs4713688	0.85[AFR][1000 genomes]
rs487835	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996878	0.87[EUR][1000 genomes]
rs4996879	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs530614	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs549652	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs570749	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597386	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs602399	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs652049	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs680608	0.94[ASN][1000 genomes]
rs684119	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs688209	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6913517	1.00[JPT][hapmap]
rs6915136	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6921772	0.87[EUR][1000 genomes]
rs7449707	0.81[EUR][1000 genomes]
rs751727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756138	0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs756139	0.85[ASW][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs764753	1.00[JPT][hapmap]
rs7739273	0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs791904	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9380379	0.84[EUR][1000 genomes]
rs942496	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs943463	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs943464	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943465	0.84[EUR][1000 genomes]
rs943473	0.87[EUR][1000 genomes]
rs943476	0.92[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs9461905	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9461907	0.90[EUR][1000 genomes]
rs9469542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs943472	C6orf125	cis	cerebellum	SCAN
rs943472	RXRB	cis	Skin Sun Exposed Lower leg	GTEx
rs943472	BAK1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33730000-33738600	Weak transcription	A549	lung
2	chr6:33730600-33738600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:33730800-33738600	Weak transcription	Liver	Liver
4	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:33735000-33739600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:33735200-33740000	Enhancers	Fetal Lung	lung
7	chr6:33735400-33739600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr6:33735800-33738800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr6:33736000-33739600	Enhancers	Colon Smooth Muscle	Colon
10	chr6:33736200-33738600	Enhancers	HSMM	muscle
11	chr6:33736200-33738800	Enhancers	Stomach Smooth Muscle	stomach
12	chr6:33736200-33739200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:33736200-33739600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:33736200-33740600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:33736400-33738800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr6:33736400-33739600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:33736400-33739600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:33736400-33739600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:33736400-33740000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:33736600-33738600	Weak transcription	Thymus	Thymus
21	chr6:33736600-33739000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:33736600-33740000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr6:33736600-33740000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:33736600-33740000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:33736600-33740200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:33736600-33740200	Enhancers	HUVEC	blood vessel
27	chr6:33736800-33739600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:33736800-33740000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:33736800-33740000	Weak transcription	GM12878-XiMat	blood
30	chr6:33736800-33740200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:33736800-33741000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:33736800-33743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:33737000-33740000	Weak transcription	HepG2	liver
34	chr6:33737200-33738600	Enhancers	Fetal Intestine Small	intestine
35	chr6:33737400-33739600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:33737400-33739600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:33737400-33739800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr6:33737400-33739800	Enhancers	NHLF	lung
39	chr6:33737400-33740200	Enhancers	NH-A	brain
40	chr6:33737600-33738600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:33737600-33739000	Enhancers	Aorta	Aorta
42	chr6:33737600-33739000	Enhancers	Lung	lung
43	chr6:33737600-33739600	Enhancers	Brain Hippocampus Middle	brain
44	chr6:33737600-33739600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr6:33737600-33739800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr6:33737600-33740000	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:33737600-33740000	Weak transcription	Dnd41	blood
48	chr6:33737600-33740200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr6:33737600-33740600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:33737800-33738800	Enhancers	Ovary	ovary

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