Variant report

Variant	rs1871499
Chromosome Location	chr15:59954723-59954724
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59954230-59955016	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:59954509-59955077	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59953943..59955964-chr15:59959254..59962157,2	K562	blood:
2	chr15:59953614..59955530-chr15:59965448..59967216,2	K562	blood:
3	chr15:59953267..59956180-chr15:59978902..59983240,4	K562	blood:
4	chr15:59949015..59951942-chr15:59953463..59956505,3	MCF-7	breast:
5	chr15:59953943..59956937-chr15:59959254..59962353,4	K562	blood:
6	chr15:59947891..59951235-chr15:59952580..59954816,3	K562	blood:
7	chr15:59952501..59955288-chr15:59979374..59982018,3	K562	blood:

No data

Variant related genes	Relation type
GTF2A2	TF binding region
ENSG00000259238	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1002181	0.88[EUR][1000 genomes]
rs10152209	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10152414	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10152415	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10152509	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10162629	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1046053	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1057059	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11071465	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11071468	0.88[EUR][1000 genomes]
rs11071469	0.88[EUR][1000 genomes]
rs1135148	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11634067	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11637071	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853610	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11854063	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441240	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12593480	0.88[EUR][1000 genomes]
rs12708458	0.86[EUR][1000 genomes]
rs12708459	0.86[EUR][1000 genomes]
rs12902582	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12902774	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903647	0.85[EUR][1000 genomes]
rs12906392	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907554	0.87[EUR][1000 genomes]
rs12907641	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12909005	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912652	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531638	0.83[EUR][1000 genomes]
rs1531639	0.83[EUR][1000 genomes]
rs1552031	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1871500	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1871503	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871504	0.89[CHB][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs1979422	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2101019	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2170062	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2306354	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306355	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2307272	0.87[EUR][1000 genomes]
rs2307273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307275	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2414638	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28671744	0.85[EUR][1000 genomes]
rs2899649	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34797071	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34894301	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3825870	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4270113	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4533213	0.87[EUR][1000 genomes]
rs4774340	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4774341	0.87[EUR][1000 genomes]
rs4775191	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775195	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4775197	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151441	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs6151458	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6151459	0.81[EUR][1000 genomes]
rs6151460	0.87[EUR][1000 genomes]
rs6151461	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6151462	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6151467	0.87[EUR][1000 genomes]
rs6151470	0.87[EUR][1000 genomes]
rs6151472	0.85[EUR][1000 genomes]
rs6151474	0.87[EUR][1000 genomes]
rs6151477	0.87[EUR][1000 genomes]
rs6151483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151486	0.87[EUR][1000 genomes]
rs6151487	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151501	0.86[EUR][1000 genomes]
rs6151503	0.88[EUR][1000 genomes]
rs6151504	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6151506	0.88[EUR][1000 genomes]
rs6151510	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]
rs6151514	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6151525	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151528	0.86[EUR][1000 genomes]
rs6151529	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6151532	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6151533	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6151535	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6151536	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6151542	0.88[EUR][1000 genomes]
rs6151545	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6151551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151553	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151557	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151565	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151568	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151570	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151571	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151574	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151576	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151580	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151581	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151586	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151588	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151589	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6151590	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012358	0.83[EUR][1000 genomes]
rs62015260	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62015289	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494127	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6494128	0.83[EUR][1000 genomes]
rs6494130	0.83[EUR][1000 genomes]
rs6494131	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6494133	0.89[EUR][1000 genomes]
rs67697180	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67820349	0.88[EUR][1000 genomes]
rs7162964	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7164756	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7172270	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7173827	0.81[JPT][hapmap];0.90[YRI][hapmap]
rs7178050	0.83[EUR][1000 genomes]
rs7178211	0.81[JPT][hapmap];0.90[YRI][hapmap]
rs7180408	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7182962	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs722163	0.87[EUR][1000 genomes]
rs722164	0.87[EUR][1000 genomes]
rs7497974	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7882	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033161	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8035465	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8040114	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041394	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1871499	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949400-59960200	Weak transcription	Fetal Heart	heart
2	chr15:59949800-59957200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:59949800-59957200	Weak transcription	Spleen	Spleen
4	chr15:59949800-59963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59949800-59964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:59949800-59968000	Weak transcription	Stomach Mucosa	stomach
7	chr15:59949800-59968400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:59950000-59963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:59950200-59954800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:59950200-59955200	Weak transcription	Fetal Brain Female	brain
12	chr15:59950200-59955400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:59950200-59955600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:59950200-59955800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:59950200-59956800	Weak transcription	Fetal Intestine Small	intestine
16	chr15:59950200-59956800	Weak transcription	Fetal Stomach	stomach
17	chr15:59950200-59956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:59950200-59957000	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:59950200-59958400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:59950200-59959200	Weak transcription	Fetal Brain Male	brain
21	chr15:59950200-59960200	Weak transcription	Colonic Mucosa	Colon
22	chr15:59950200-59961200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:59950200-59963400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:59950200-59963400	Weak transcription	Brain Angular Gyrus	brain
25	chr15:59950200-59963400	Weak transcription	Ovary	ovary
26	chr15:59950200-59964000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:59950200-59964000	Weak transcription	Gastric	stomach
28	chr15:59950200-59964000	Weak transcription	Lung	lung
29	chr15:59950200-59964000	Weak transcription	Small Intestine	intestine
30	chr15:59950200-59967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:59950200-59968400	Weak transcription	Right Ventricle	heart
32	chr15:59950200-59968800	Weak transcription	Aorta	Aorta
33	chr15:59950400-59954800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:59950400-59954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:59950400-59956800	Weak transcription	Thymus	Thymus
36	chr15:59950400-59958400	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:59950400-59960200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:59950400-59964000	Weak transcription	Pancreas	Pancrea
39	chr15:59950400-59964000	Weak transcription	Psoas Muscle	Psoas
40	chr15:59950400-59965600	Weak transcription	Brain Substantia Nigra	brain
41	chr15:59950400-59968800	Weak transcription	Esophagus	oesophagus
42	chr15:59950400-59979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:59950600-59955200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:59950600-59957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:59950800-59956600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:59950800-59961600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:59951000-59978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:59951200-59958600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:59951400-59956400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:59951400-59960600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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