Variant report

Variant	rs4294450
Chromosome Location	chr1:173389640-173389641
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173389394..173390067-chr1:173398715..173399226,2	MCF-7	breast:
2	chr1:172713808..172714358-chr1:173389226..173389934,2	K562	blood:
3	chr1:173388744..173390977-chr1:173445592..173447369,2	MCF-7	breast:
4	chr1:173384031..173386139-chr1:173387670..173391355,5	K562	blood:
5	chr1:173389159..173390025-chr1:173793879..173794799,2	MCF-7	breast:
6	chr1:173383188..173385613-chr1:173387916..173390631,2	K562	blood:
7	chr1:173389064..173389771-chr1:174186582..174187512,2	MCF-7	breast:
8	chr1:173224094..173224760-chr1:173389388..173389899,2	MCF-7	breast:
9	chr1:172713852..172714797-chr1:173389258..173389975,2	MCF-7	breast:
10	chr1:173389092..173391393-chr1:173792851..173794352,2	K562	blood:
11	chr1:173388591..173390772-chr1:173793022..173795390,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117592	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10737301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753079	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753080	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798290	0.80[CHB][hapmap]
rs10912624	1.00[CHB][hapmap]
rs10912626	1.00[CHB][hapmap]
rs10912641	0.95[CHB][hapmap]
rs10912643	1.00[CHB][hapmap]
rs12026427	1.00[CHB][hapmap]
rs12026677	1.00[CHB][hapmap]
rs12037210	1.00[CHB][hapmap]
rs12039524	0.82[CEU][hapmap]
rs12058528	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12065426	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs12077271	0.81[EUR][1000 genomes]
rs12080769	0.87[EUR][1000 genomes]
rs12565753	0.82[EUR][1000 genomes]
rs12724371	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12744504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12745058	0.82[EUR][1000 genomes]
rs12753631	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760501	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1461014	1.00[CHB][hapmap]
rs1886639	1.00[CHB][hapmap]
rs33942654	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33951697	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34025182	0.87[EUR][1000 genomes]
rs34259759	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34296122	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34331061	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34332254	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34919111	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35065145	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35379498	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35607505	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35632090	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35831548	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35845062	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36058163	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3934575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244196	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4310474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4462186	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4539167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57032935	0.86[EUR][1000 genomes]
rs61826747	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826748	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826749	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826753	0.92[ASN][1000 genomes]
rs61828886	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61828887	0.84[AMR][1000 genomes]
rs61828888	0.84[AMR][1000 genomes]
rs6425232	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425251	0.80[CHB][hapmap]
rs6660804	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66683313	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670071	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671141	0.94[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.92[EUR][1000 genomes]
rs6687872	1.00[CHB][hapmap]
rs6696443	0.84[EUR][1000 genomes]
rs6699094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702835	0.84[CEU][hapmap]
rs68193118	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72637251	0.86[ASN][1000 genomes]
rs7314	0.84[CEU][hapmap]
rs7413754	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7516544	0.82[EUR][1000 genomes]
rs7520641	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521536	0.85[EUR][1000 genomes]
rs7524403	0.85[EUR][1000 genomes]
rs7524592	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs7525100	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7529089	0.87[EUR][1000 genomes]
rs7529377	0.87[EUR][1000 genomes]
rs7530469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540065	0.84[CEU][hapmap]
rs7541082	0.80[CHB][hapmap]
rs7549074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912767	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4294450	PRDX6	cis	cerebellum	SCAN
rs4294450	PRDX6	cis	parietal	SCAN
rs4294450	RC3H1	cis	parietal	SCAN
rs4294450	TNFSF4	cis	parietal	SCAN
rs4294450	DARS2	cis	parietal	SCAN
rs4294450	DARS2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173372000-173398600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:173375200-173398600	Weak transcription	Esophagus	oesophagus
3	chr1:173376200-173429000	Weak transcription	Gastric	stomach
4	chr1:173376400-173400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:173376600-173392600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:173378400-173398400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:173379000-173398400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:173379200-173393200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:173380200-173391200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:173380200-173398400	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:173380200-173398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:173380200-173398600	Weak transcription	Psoas Muscle	Psoas
13	chr1:173380400-173392600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:173380400-173398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:173380400-173398600	Weak transcription	Thymus	Thymus
16	chr1:173380400-173398800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:173383000-173390600	Weak transcription	Ovary	ovary
18	chr1:173383000-173398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:173385600-173391400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:173385600-173398600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:173385600-173398600	Weak transcription	Spleen	Spleen
22	chr1:173386000-173397800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:173387600-173429000	Weak transcription	Lung	lung
24	chr1:173387800-173391000	Weak transcription	Primary T cells from cord blood	blood
25	chr1:173387800-173391400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:173387800-173398400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:173387800-173398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:173388000-173390400	Weak transcription	HSMMtube	muscle
29	chr1:173388000-173398400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:173388000-173398400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:173388000-173398600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:173388200-173389800	Enhancers	GM12878-XiMat	blood
33	chr1:173388200-173390600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:173388200-173391200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:173389000-173389800	Enhancers	K562	blood
36	chr1:173389000-173390000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:173389000-173390000	Enhancers	Adipose Nuclei	Adipose
38	chr1:173389200-173390000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:173389200-173390000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:173389200-173390000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr1:173389200-173390000	Enhancers	Osteobl	bone
42	chr1:173389200-173390800	Enhancers	HSMM	muscle
43	chr1:173389400-173389800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr1:173389400-173389800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:173389400-173389800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr1:173389400-173389800	Enhancers	Fetal Lung	lung
47	chr1:173389400-173390000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:173389400-173390000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:173389400-173390000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr1:173389400-173390000	Enhancers	Primary T helper cells fromperipheralblood	blood

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