Variant report

Variant	rs10912618
Chromosome Location	chr1:173399734-173399735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173392536..173394729-chr1:173398389..173400168,2	MCF-7	breast:
2	chr1:173396801..173401606-chr1:173443939..173449488,12	K562	blood:
3	chr1:173397836..173400483-chr1:173795399..173797662,2	K562	blood:
4	chr1:173396850..173400965-chr1:173792784..173795778,4	MCF-7	breast:
5	chr1:173397598..173400442-chr1:173792113..173794367,4	MCF-7	breast:
6	chr1:173398763..173400858-chr1:173682835..173685782,2	K562	blood:
7	chr1:173398704..173401642-chr1:173829873..173832567,2	MCF-7	breast:
8	chr1:173398971..173403137-chr1:173453478..173457136,4	K562	blood:
9	chr1:173398890..173402305-chr1:173404603..173408427,6	K562	blood:
10	chr1:173397788..173400403-chr1:173827176..173829945,2	K562	blood:
11	chr1:173398919..173401669-chr1:173825835..173827646,3	MCF-7	breast:
12	chr1:173398813..173400471-chr1:173837965..173839630,2	K562	blood:
13	chr1:173396632..173402246-chr1:173834991..173837627,5	MCF-7	breast:
14	chr1:173399114..173400680-chr1:173792617..173795012,2	K562	blood:
15	chr1:173399312..173401264-chr1:173445361..173448532,4	MCF-7	breast:
16	chr1:173397246..173400257-chr1:173445206..173450415,6	K562	blood:
17	chr1:173397788..173400470-chr1:173826012..173828676,2	K562	blood:
18	chr1:173397648..173401929-chr1:173831586..173837158,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000120334	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10753081	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092383	0.81[CHB][hapmap]
rs12140760	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs4255417	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4276950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325171	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916220	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916355	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916359	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916361	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4916363	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55654074	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425231	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696012	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6702835	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7314	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap]
rs7537938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540065	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs7556003	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425719	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425723	0.86[ASN][1000 genomes]
rs9425724	0.86[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	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10912618	TNFSF4	cis	parietal	SCAN
rs10912618	PRDX6	cis	cerebellum	SCAN
rs10912618	PRDX6	cis	parietal	SCAN
rs10912618	FASLG	cis	cerebellum	SCAN
rs10912618	GPR52	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173376200-173429000	Weak transcription	Gastric	stomach
2	chr1:173376400-173400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:173387600-173429000	Weak transcription	Lung	lung
4	chr1:173389600-173400600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:173391800-173429000	Weak transcription	Ovary	ovary
6	chr1:173394800-173400600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:173398400-173399800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:173398400-173399800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:173398400-173399800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:173398400-173399800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:173398400-173399800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:173398400-173399800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:173398400-173399800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:173398400-173399800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:173398400-173399800	Flanking Active TSS	Osteobl	bone
16	chr1:173398400-173400000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:173398400-173400000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:173398400-173400200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:173398400-173400200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:173398400-173400200	Flanking Active TSS	K562	blood
21	chr1:173398400-173400600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:173398400-173400800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:173398400-173400800	Enhancers	Stomach Mucosa	stomach
24	chr1:173398400-173401200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:173398600-173399800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:173398600-173399800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:173398600-173399800	Enhancers	Liver	Liver
28	chr1:173398600-173399800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:173398600-173399800	Flanking Active TSS	Hela-S3	cervix
30	chr1:173398600-173399800	Flanking Active TSS	NH-A	brain
31	chr1:173398600-173399800	Flanking Active TSS	NHDF-Ad	bronchial
32	chr1:173398600-173399800	Flanking Active TSS	NHLF	lung
33	chr1:173398600-173400000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:173398600-173400000	Enhancers	Fetal Brain Female	brain
35	chr1:173398600-173400000	Enhancers	Placenta	Placenta
36	chr1:173398600-173400400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:173398600-173400600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:173398600-173400800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:173398600-173400800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr1:173398600-173401000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:173398800-173400000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr1:173398800-173400000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:173398800-173400000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr1:173398800-173400400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:173398800-173400600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:173398800-173400600	Weak transcription	Left Ventricle	heart
47	chr1:173399000-173399800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:173399000-173400000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:173399000-173400400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:173399200-173399800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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