Variant report

Variant	rs1536500
Chromosome Location	chr6:33723383-33723384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33716774..33719604-chr6:33722894..33724395,2	K562	blood:
2	chr6:33717351..33720634-chr6:33722895..33725009,3	K562	blood:
3	chr6:33676238..33679184-chr6:33722714..33724604,2	MCF-7	breast:
4	chr6:33673241..33675350-chr6:33722857..33725675,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	0.94[CEU][hapmap]
rs10947436	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs10947446	0.83[CEU][hapmap]
rs11751943	0.94[EUR][1000 genomes]
rs1318691	0.82[EUR][1000 genomes]
rs1536501	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs1547668	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1998949	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2182658	0.82[EUR][1000 genomes]
rs2182659	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs2395401	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs2395446	0.81[EUR][1000 genomes]
rs2395447	0.91[EUR][1000 genomes]
rs2395448	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2967	1.00[JPT][hapmap]
rs4711350	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs4713676	0.91[EUR][1000 genomes]
rs487835	0.83[EUR][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996878	0.92[EUR][1000 genomes]
rs4996879	0.92[EUR][1000 genomes]
rs530614	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs549652	1.00[JPT][hapmap]
rs570749	0.82[EUR][1000 genomes]
rs597386	1.00[JPT][hapmap]
rs602399	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[JPT][hapmap]
rs652049	0.89[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	1.00[JPT][hapmap]
rs684119	1.00[JPT][hapmap]
rs688209	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[JPT][hapmap]
rs6921772	0.82[EUR][1000 genomes]
rs7449707	0.89[EUR][1000 genomes]
rs751727	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs756138	0.82[EUR][1000 genomes]
rs756139	0.82[EUR][1000 genomes]
rs764753	1.00[JPT][hapmap]
rs7739273	0.82[EUR][1000 genomes]
rs791904	0.83[EUR][1000 genomes]
rs9380379	0.82[EUR][1000 genomes]
rs942496	0.83[CEU][hapmap]
rs943463	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943464	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs943465	0.88[EUR][1000 genomes]
rs943472	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs943473	0.82[EUR][1000 genomes]
rs943476	0.82[EUR][1000 genomes]
rs9461905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461907	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1536500	BAK1	cis	Skin Sun Exposed Lower leg	GTEx
rs1536500	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr6:33719200-33723600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:33719600-33729000	Weak transcription	Right Atrium	heart
5	chr6:33719800-33727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:33719800-33729200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:33720200-33728000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:33720200-33730600	Weak transcription	Spleen	Spleen
9	chr6:33720400-33728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:33720600-33729400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:33720800-33726200	Weak transcription	Fetal Lung	lung
12	chr6:33721000-33724000	Weak transcription	Stomach Mucosa	stomach
13	chr6:33721000-33727000	Weak transcription	Fetal Intestine Small	intestine
14	chr6:33721000-33729400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:33721200-33728600	Weak transcription	Fetal Thymus	thymus
16	chr6:33721400-33724400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:33722200-33723600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:33722200-33723600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:33722200-33725400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:33722400-33723600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:33722400-33723800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:33722600-33723400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:33722600-33723600	Enhancers	GM12878-XiMat	blood
24	chr6:33722800-33723600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:33722800-33723600	Enhancers	Fetal Muscle Leg	muscle
26	chr6:33723000-33723400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:33723000-33723400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:33723000-33723400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr6:33723000-33723600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:33723000-33723600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:33723200-33725600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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