Variant report

Variant	rs6151510
Chromosome Location	chr15:59972372-59972373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59972354-59972941	A549	lung:	n/a	n/a
2	POLR2A	chr15:59972164-59972969	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59958616..59963871-chr15:59968752..59974672,6	K562	blood:
2	chr15:59970781..59973494-chr15:59980091..59981802,2	MCF-7	breast:

Variant related genes	Relation type
BNIP2	TF binding region
ENSG00000259238	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1002181	0.83[EUR][1000 genomes]
rs10152209	0.90[CEU][hapmap]
rs10152415	0.90[CEU][hapmap]
rs10152509	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10162629	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1046053	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1057059	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11071465	0.91[CEU][hapmap]
rs11071468	0.82[EUR][1000 genomes]
rs11071469	0.82[EUR][1000 genomes]
rs1135148	0.91[CEU][hapmap]
rs11637071	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637359	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11854063	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs12593480	0.82[EUR][1000 genomes]
rs12902582	0.95[CEU][hapmap]
rs12902774	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907554	0.81[EUR][1000 genomes]
rs12907641	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909005	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912652	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1552031	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1871499	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871500	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs1871503	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871504	0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs1979422	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2101019	0.91[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170062	0.85[EUR][1000 genomes]
rs2306354	0.91[CHB][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs2306355	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2307272	0.83[EUR][1000 genomes]
rs2307273	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307275	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2414638	0.83[EUR][1000 genomes]
rs2899649	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784389	0.82[CEU][hapmap]
rs3825870	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4270113	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4533213	0.82[EUR][1000 genomes]
rs4774340	0.90[CEU][hapmap]
rs4775195	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4775197	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151441	0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs6151458	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151460	0.82[EUR][1000 genomes]
rs6151461	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151462	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151467	0.82[EUR][1000 genomes]
rs6151470	0.82[EUR][1000 genomes]
rs6151472	0.81[EUR][1000 genomes]
rs6151474	0.82[EUR][1000 genomes]
rs6151477	0.82[EUR][1000 genomes]
rs6151483	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151486	0.82[EUR][1000 genomes]
rs6151487	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151501	0.81[EUR][1000 genomes]
rs6151503	0.83[EUR][1000 genomes]
rs6151504	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151506	0.83[EUR][1000 genomes]
rs6151514	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151525	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151528	0.82[EUR][1000 genomes]
rs6151529	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151532	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151533	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6151535	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151536	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151542	0.82[EUR][1000 genomes]
rs6151545	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6151551	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151553	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151557	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151561	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151565	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151568	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151570	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151571	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151574	0.81[EUR][1000 genomes]
rs6151576	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151580	0.83[EUR][1000 genomes]
rs6151586	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151588	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6151589	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs6151590	0.81[EUR][1000 genomes]
rs6151592	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62015260	0.86[EUR][1000 genomes]
rs62015289	0.82[EUR][1000 genomes]
rs6494127	0.84[EUR][1000 genomes]
rs6494131	0.91[CEU][hapmap]
rs6494133	0.81[EUR][1000 genomes]
rs67697180	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67820349	0.81[EUR][1000 genomes]
rs7162964	0.90[CEU][hapmap]
rs7164756	0.91[CEU][hapmap]
rs7172270	0.84[EUR][1000 genomes]
rs7173827	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs7178211	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs7180408	0.91[CEU][hapmap]
rs7182962	0.91[CEU][hapmap]
rs722163	0.82[EUR][1000 genomes]
rs722164	0.82[EUR][1000 genomes]
rs7497974	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7882	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033161	0.81[EUR][1000 genomes]
rs8035465	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8040114	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041394	0.91[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv523274	chr15:59971635-59973563	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6151510	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:59950400-59979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59951000-59978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:59951400-59972600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:59951400-59973600	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr15:59951400-59973600	Strong transcription	HSMM	muscle
7	chr15:59951400-59975000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:59951400-59975200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:59951400-59975400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:59951400-59976000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:59951400-59978800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:59951600-59976400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr15:59951800-59975000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:59951800-59975600	Strong transcription	Primary B cells from cord blood	blood
15	chr15:59952000-59975600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:59952000-59976600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:59952000-59977800	Strong transcription	Hela-S3	cervix
18	chr15:59952200-59974800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:59952200-59974800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr15:59952200-59975400	Strong transcription	Fetal Thymus	thymus
21	chr15:59952200-59975600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:59952200-59976400	Strong transcription	Placenta	Placenta
23	chr15:59952400-59974800	Strong transcription	Fetal Intestine Large	intestine
24	chr15:59952400-59975800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:59952400-59977400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:59952400-59978600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:59952600-59975600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr15:59952600-59976000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:59952600-59976800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:59952800-59977400	Strong transcription	Dnd41	blood
31	chr15:59954200-59973600	Strong transcription	A549	lung
32	chr15:59954200-59975200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:59955000-59974400	Strong transcription	Adipose Nuclei	Adipose
34	chr15:59955800-59974800	Strong transcription	Osteobl	bone
35	chr15:59956200-59974800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:59956200-59975600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:59956600-59975600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:59957000-59975600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:59957800-59974800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:59957800-59977200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:59959000-59974200	Strong transcription	HSMMtube	muscle
42	chr15:59959200-59974200	Strong transcription	NH-A	brain
43	chr15:59959200-59975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:59959600-59975400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:59959800-59974000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:59959800-59975600	Strong transcription	GM12878-XiMat	blood
47	chr15:59960000-59974000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:59960000-59974400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr15:59960000-59974400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:59960000-59974400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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