Variant report

Variant	rs2457497
Chromosome Location	chr15:82431219-82431220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:82336645..82339612-chr15:82430236..82432399,2	MCF-7	breast:
2	chr15:82337367..82339936-chr15:82429505..82432664,3	MCF-7	breast:
3	chr15:82423103..82426448-chr15:82429723..82433616,4	K562	blood:
4	chr15:82403068..82405226-chr15:82430485..82432551,2	K562	blood:

Variant related genes	Relation type
ENSG00000183496	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11073036	0.93[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11630197	0.91[ASW][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs11631813	0.81[ASW][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs11639440	0.89[JPT][hapmap]
rs11854289	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11854483	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12324875	0.90[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1501367	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1566561	0.84[ASN][1000 genomes]
rs16973457	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1948741	0.81[ASN][1000 genomes]
rs1948742	0.85[CHB][hapmap]
rs1972460	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs2016372	0.85[ASN][1000 genomes]
rs2047679	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2134046	0.84[JPT][hapmap]
rs2665103	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3759800	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3902959	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4238534	0.91[ASW][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs4267268	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4296215	0.93[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs4778986	0.92[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4778987	0.90[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs61554133	0.81[ASN][1000 genomes]
rs72749540	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72749543	0.89[EUR][1000 genomes]
rs72749557	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72749560	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72749561	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72749564	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72749586	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7403244	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs8027301	1.00[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8027661	1.00[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8030210	0.81[ASN][1000 genomes]
rs8030250	0.93[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs8032633	0.81[ASN][1000 genomes]
rs8033313	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs905450	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972440	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833067	chr15:82234980-82450485	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2457497	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs2457497	EFTUD1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82399000-82452200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:82408000-82443600	Weak transcription	Aorta	Aorta
3	chr15:82408400-82431800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:82408800-82432400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:82415600-82431800	Weak transcription	HUVEC	blood vessel
6	chr15:82416200-82443400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:82416200-82452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:82416400-82431400	Strong transcription	Primary T cells from cord blood	blood
9	chr15:82416400-82454000	Weak transcription	Colonic Mucosa	Colon
10	chr15:82416600-82443800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:82419200-82470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:82420000-82457000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:82420200-82431400	Strong transcription	Dnd41	blood
14	chr15:82420200-82432000	Weak transcription	Brain Anterior Caudate	brain
15	chr15:82420400-82458400	Weak transcription	HepG2	liver
16	chr15:82420600-82436200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:82420800-82431400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:82420800-82432000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:82421200-82432200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:82421200-82443800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:82421400-82439000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:82422400-82432000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:82422600-82432000	Weak transcription	Brain Substantia Nigra	brain
24	chr15:82423000-82432400	Weak transcription	Ovary	ovary
25	chr15:82423000-82443600	Weak transcription	Right Ventricle	heart
26	chr15:82423000-82443800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:82423200-82443800	Weak transcription	Psoas Muscle	Psoas
28	chr15:82423200-82454800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:82423600-82432000	Weak transcription	Brain Angular Gyrus	brain
30	chr15:82424400-82431400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr15:82425000-82443400	Weak transcription	Fetal Intestine Small	intestine
32	chr15:82425400-82435800	Weak transcription	Fetal Stomach	stomach
33	chr15:82425400-82436200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:82425600-82438600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:82425600-82439000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:82425800-82443200	Weak transcription	Fetal Brain Female	brain
37	chr15:82426000-82457000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:82426400-82431800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:82426400-82435600	Weak transcription	Lung	lung
40	chr15:82426800-82443400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:82426800-82443600	Weak transcription	Gastric	stomach
42	chr15:82426800-82443600	Weak transcription	Spleen	Spleen
43	chr15:82427000-82432000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:82427000-82443400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:82427200-82443600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:82427600-82443000	Weak transcription	Brain Germinal Matrix	brain
47	chr15:82427600-82456600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:82427800-82431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:82427800-82431600	Strong transcription	A549	lung
50	chr15:82428000-82432600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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