Variant report

Variant	rs1536501
Chromosome Location	chr6:33727885-33727886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33674794..33680843-chr6:33726905..33731016,6	MCF-7	breast:
2	chr6:33727358..33730164-chr6:33732846..33736236,4	K562	blood:
3	chr6:33727069..33729812-chr6:33754645..33756635,3	MCF-7	breast:
4	chr6:33725418..33728218-chr6:33736581..33739360,2	MCF-7	breast:
5	chr6:33712420..33715409-chr6:33723991..33728116,4	MCF-7	breast:
6	chr6:33725421..33728114-chr6:33818801..33821160,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161896	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	0.89[CEU][hapmap]
rs10947436	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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947446	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes]
rs11751943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318691	0.85[EUR][1000 genomes]
rs1536500	0.96[EUR][1000 genomes]
rs1547668	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951930	0.81[AFR][1000 genomes]
rs1998949	0.89[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs2182658	0.92[ASW][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs2182659	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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395401	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395446	0.85[EUR][1000 genomes]
rs2395447	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395448	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2967	1.00[JPT][hapmap]
rs3957165	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4711350	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713676	0.88[EUR][1000 genomes]
rs4713687	0.83[AFR][1000 genomes]
rs4713688	0.83[AFR][1000 genomes]
rs487835	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996878	0.90[EUR][1000 genomes]
rs4996879	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs530614	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549652	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs570749	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs597386	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs602399	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs652049	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs680608	0.94[ASN][1000 genomes]
rs684119	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs688209	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6921772	0.85[EUR][1000 genomes]
rs7449707	0.87[EUR][1000 genomes]
rs751727	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756138	0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs756139	0.92[ASW][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs764753	1.00[JPT][hapmap]
rs7739273	0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs7752348	0.81[EUR][1000 genomes]
rs791904	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9380379	0.83[EUR][1000 genomes]
rs942496	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.83[AFR][1000 genomes]
rs943463	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs943464	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943465	0.88[EUR][1000 genomes]
rs943472	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]
rs943473	0.85[EUR][1000 genomes]
rs943476	1.00[ASW][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs9461905	0.94[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs9461907	0.97[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
rs1536501	BAK1	cis	Skin Sun Exposed Lower leg	GTEx
rs1536501	RXRB	cis	Skin Sun Exposed Lower leg	GTEx
rs1536501	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33715200-33737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33715600-33729400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:33719600-33729000	Weak transcription	Right Atrium	heart
4	chr6:33719800-33729200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:33720200-33728000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:33720200-33730600	Weak transcription	Spleen	Spleen
7	chr6:33720400-33728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:33720600-33729400	Weak transcription	Fetal Intestine Large	intestine
9	chr6:33721000-33729400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:33721200-33728600	Weak transcription	Fetal Thymus	thymus
11	chr6:33723400-33729800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:33723400-33736600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:33723600-33728200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:33723600-33728800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:33723600-33729000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:33724000-33730200	Enhancers	Stomach Mucosa	stomach
17	chr6:33725000-33728800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:33725200-33729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:33725200-33729600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:33725200-33729800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:33726000-33731000	Enhancers	Fetal Stomach	stomach
22	chr6:33726200-33729600	Enhancers	Liver	Liver
23	chr6:33726200-33731000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:33726200-33731400	Enhancers	Fetal Lung	lung
25	chr6:33726400-33729200	Weak transcription	Placenta	Placenta
26	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:33727000-33728000	Weak transcription	Fetal Kidney	kidney
28	chr6:33727000-33728000	Enhancers	Hela-S3	cervix
29	chr6:33727000-33730800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:33727200-33729000	Weak transcription	Fetal Intestine Small	intestine
31	chr6:33727400-33728800	Weak transcription	A549	lung
32	chr6:33727600-33728200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr6:33727800-33728000	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr6:33727800-33729000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:33727800-33729600	Enhancers	Skeletal Muscle Female	skeletal muscle

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