Variant report

Variant	rs7167638
Chromosome Location	chr15:59509144-59509145
allele	A/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	chr15:59508902-59509514	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:59508900-59509296	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:59508992-59509497	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:59509125-59509426	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:59509062-59509414	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:59509109-59509487	A549	lung:	n/a	n/a
7	POLR2A	chr15:59509070-59509476	GM12891	blood:	n/a	n/a
8	POLR2A	chr15:59508915-59509952	GM12891	blood:	n/a	n/a
9	POLR2A	chr15:59509092-59509447	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:59509065-59509497	GM12891	blood:	n/a	n/a
11	POLR2A	chr15:59508912-59509459	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:59508996-59509490	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
RNU4-80P	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11634548	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11638386	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438740	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2230155	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306779	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306780	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35481817	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794491	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3794492	0.95[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794493	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816813	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775131	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775135	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73422960	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv2760385	chr15:59506428-59513647	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
2	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
3	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr15:59475800-59517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:59483200-59514000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:59485400-59515400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:59485600-59521200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:59487800-59524400	Weak transcription	Small Intestine	intestine
9	chr15:59489800-59512600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:59489800-59515600	Weak transcription	Right Atrium	heart
11	chr15:59490200-59510800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:59492000-59521600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr15:59493000-59512000	Strong transcription	HSMM	muscle
14	chr15:59493000-59513800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:59493200-59513600	Strong transcription	Osteobl	bone
16	chr15:59493200-59513800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:59493200-59514400	Strong transcription	HMEC	breast
18	chr15:59493200-59523200	Strong transcription	Hela-S3	cervix
19	chr15:59494800-59514200	Strong transcription	A549	lung
20	chr15:59496800-59515200	Weak transcription	Spleen	Spleen
21	chr15:59496800-59515600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:59496800-59522000	Strong transcription	NHEK	skin
23	chr15:59497000-59514600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:59497000-59524800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:59497200-59517600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:59498000-59516000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:59498800-59522000	Strong transcription	GM12878-XiMat	blood
28	chr15:59499200-59512600	Strong transcription	Fetal Intestine Large	intestine
29	chr15:59500000-59509200	Weak transcription	Psoas Muscle	Psoas
30	chr15:59500000-59509600	Weak transcription	Esophagus	oesophagus
31	chr15:59500000-59513600	Weak transcription	Fetal Kidney	kidney
32	chr15:59500000-59515000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:59500000-59515000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:59500000-59517600	Weak transcription	Fetal Lung	lung
35	chr15:59500000-59524400	Weak transcription	Right Ventricle	heart
36	chr15:59500600-59524600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:59501000-59509200	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:59501200-59509200	Weak transcription	Fetal Stomach	stomach
39	chr15:59501200-59509800	Weak transcription	Lung	lung
40	chr15:59501200-59510400	Weak transcription	Brain Angular Gyrus	brain
41	chr15:59501200-59514200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:59501200-59515000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:59501200-59515000	Weak transcription	Pancreas	Pancrea
44	chr15:59501200-59521400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:59501200-59523400	Weak transcription	Ovary	ovary
46	chr15:59501200-59525600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:59501400-59509200	Weak transcription	HepG2	liver
48	chr15:59501400-59514200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:59502400-59510600	Strong transcription	Placenta	Placenta
50	chr15:59502400-59513400	Strong transcription	NHDF-Ad	bronchial

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