Variant report

Variant	rs6432039
Chromosome Location	chr2:9960111-9960112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9957012..9961532-chr2:9962183..9964607,4	MCF-7	breast:
2	chr2:9959578..9960574-chr5:133706757..133707404,2	Hela-S3	cervix:
3	chr2:9937133..9939802-chr2:9958329..9960666,2	MCF-7	breast:
4	chr2:9954879..9956876-chr2:9957733..9960340,3	K562	blood:
5	chr2:9958265..9960358-chr2:9982422..9984915,2	MCF-7	breast:
6	chr2:9952585..9955462-chr2:9959911..9962016,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119048	Chromatin interaction
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1971101	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2245344	0.90[CEU][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303914	0.86[CEU][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6432044	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv528645	chr2:9946213-9975557	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
8	nsv873622	chr2:9948404-9971366	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv873623	chr2:9949464-9964947	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv873624	chr2:9949464-9971366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv873625	chr2:9949464-9971366	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv469416	chr2:9949464-9975557	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	nsv873626	chr2:9949464-9975557	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
14	nsv873627	chr2:9949464-9982608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
15	nsv873628	chr2:9949464-9985670	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
16	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
17	nsv469427	chr2:9951970-9975557	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
18	nsv580959	chr2:9951970-9975557	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
19	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6432039	TAF1B	cis	multi-tissue	Pritchard
rs6432039	TAF1B	cis	lung	GTEx
rs6432039	TAF1B	cis	Esophagus Mucosa	GTEx
rs6432039	TAF1B	cis	lesional skin	skin_eQTL
rs6432039	TAF1B	cis	Artery Tibial	GTEx
rs6432039	TAF1B	cis	normal skin	skin_eQTL
rs6432039	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs6432039	RP11-95D17.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6432039	TAF1B	cis	Adipose Subcutaneous	GTEx
rs6432039	RP11-95D17.1	cis	lung	GTEx
rs6432039	RP11-95D17.1	cis	Esophagus Mucosa	GTEx
rs6432039	RP11-95D17.1	cis	Whole Blood	GTEx
rs6432039	TAF1B	cis	Muscle Skeletal	GTEx
rs6432039	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs6432039	TAF1B	cis	Nerve Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9954200-9964200	Weak transcription	Right Atrium	heart
2	chr2:9955200-9983000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:9958000-9960800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:9959600-9960200	Enhancers	Esophagus	oesophagus
5	chr2:9959600-9961000	Enhancers	Placenta	Placenta
6	chr2:9959600-9962400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:9959800-9960200	Enhancers	Lung	lung
8	chr2:9959800-9960200	Flanking Active TSS	NHEK	skin
9	chr2:9959800-9960400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:9959800-9960400	Flanking Active TSS	Hela-S3	cervix
11	chr2:9959800-9960800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr2:9959800-9960800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:9959800-9960800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:9959800-9960800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:9959800-9960800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:9959800-9960800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:9959800-9960800	Enhancers	Pancreas	Pancrea
18	chr2:9959800-9960800	Enhancers	A549	lung
19	chr2:9959800-9960800	Enhancers	NH-A	brain
20	chr2:9959800-9960800	Enhancers	Osteobl	bone
21	chr2:9959800-9961000	Enhancers	HMEC	breast
22	chr2:9959800-9962400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:9960000-9960200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:9960000-9960200	Enhancers	Stomach Mucosa	stomach
25	chr2:9960000-9960400	Enhancers	HSMM	muscle
26	chr2:9960000-9960600	Bivalent Enhancer	HepG2	liver
27	chr2:9960000-9960800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:9960000-9960800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr2:9960000-9960800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:9960000-9960800	Enhancers	HSMMtube	muscle
31	chr2:9960000-9961000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:9960000-9961000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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