Variant report

Variant	rs3934576
Chromosome Location	chr1:173398436-173398437
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173392536..173394729-chr1:173398389..173400168,2	MCF-7	breast:
2	chr1:173398398..173399249-chr1:173794125..173794771,2	MCF-7	breast:
3	chr1:173396801..173401606-chr1:173443939..173449488,12	K562	blood:
4	chr1:173397836..173400483-chr1:173795399..173797662,2	K562	blood:
5	chr1:173396850..173400965-chr1:173792784..173795778,4	MCF-7	breast:
6	chr1:173378019..173378602-chr1:173398305..173399235,2	MCF-7	breast:
7	chr1:173397598..173400442-chr1:173792113..173794367,4	MCF-7	breast:
8	chr1:173398302..173399200-chr1:174186558..174187278,3	MCF-7	breast:
9	chr1:173398397..173399252-chr1:173793796..173794656,6	MCF-7	breast:
10	chr1:173397788..173400403-chr1:173827176..173829945,2	K562	blood:
11	chr1:173397282..173399148-chr1:173834932..173837352,2	K562	blood:
12	chr1:173396632..173402246-chr1:173834991..173837627,5	MCF-7	breast:
13	chr1:173397246..173400257-chr1:173445206..173450415,6	K562	blood:
14	chr1:173397788..173400470-chr1:173826012..173828676,2	K562	blood:
15	chr1:173397648..173401929-chr1:173831586..173837158,8	K562	blood:

No data

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

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

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];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753079	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753080	0.95[AMR][1000 genomes];0.97[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	0.94[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];0.84[EUR][1000 genomes]
rs12080769	0.86[EUR][1000 genomes]
rs12565753	0.81[EUR][1000 genomes]
rs12724371	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12744504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12745058	0.81[EUR][1000 genomes]
rs12753631	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760501	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1461014	1.00[CHB][hapmap]
rs1886639	1.00[CHB][hapmap]
rs33942654	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33951697	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34025182	0.86[EUR][1000 genomes]
rs34259759	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34296122	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34331061	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34332254	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34919111	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35065145	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35379498	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35607505	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35632090	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35831548	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35845062	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36058163	0.89[AMR][1000 genomes];0.95[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[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];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244196	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4294450	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]
rs4310474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4462186	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4539167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57032935	0.85[EUR][1000 genomes]
rs61826747	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826748	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826749	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826753	0.92[ASN][1000 genomes]
rs61828886	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61828887	0.82[AMR][1000 genomes]
rs61828888	0.82[AMR][1000 genomes]
rs6425232	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66683313	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670071	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671141	0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.91[EUR][1000 genomes]
rs6687872	1.00[CHB][hapmap]
rs6696443	0.83[EUR][1000 genomes]
rs6699094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702835	0.84[CEU][hapmap]
rs68193118	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72637251	0.86[ASN][1000 genomes]
rs7314	0.84[CEU][hapmap]
rs7413754	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7516544	0.81[EUR][1000 genomes]
rs7520641	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521536	0.84[EUR][1000 genomes]
rs7524403	0.84[EUR][1000 genomes]
rs7524592	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs7525100	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7529089	0.86[EUR][1000 genomes]
rs7529377	0.86[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];0.89[AMR][1000 genomes];0.95[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];0.91[AMR][1000 genomes];0.95[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];0.86[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3934576	DARS2	cis	cerebellum	SCAN
rs3934576	PRDX6	cis	parietal	SCAN
rs3934576	RC3H1	cis	parietal	SCAN
rs3934576	SLC9A11	cis	parietal	SCAN
rs3934576	DARS2	cis	parietal	SCAN
rs3934576	TNFSF4	cis	parietal	SCAN
rs3934576	PRDX6	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

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	chr1:173380200-173398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:173380200-173398600	Weak transcription	Psoas Muscle	Psoas
7	chr1:173380400-173398600	Weak transcription	Thymus	Thymus
8	chr1:173380400-173398800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:173383000-173398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:173385600-173398600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:173385600-173398600	Weak transcription	Spleen	Spleen
12	chr1:173387600-173429000	Weak transcription	Lung	lung
13	chr1:173387800-173398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:173388000-173398600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:173389600-173398600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:173389600-173398600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:173389600-173398600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:173389600-173398600	Weak transcription	Left Ventricle	heart
19	chr1:173389600-173399200	Weak transcription	Pancreas	Pancrea
20	chr1:173389600-173400600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:173390000-173398600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:173390000-173398600	Weak transcription	HUVEC	blood vessel
23	chr1:173391800-173429000	Weak transcription	Ovary	ovary
24	chr1:173392000-173398600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:173392000-173398600	Weak transcription	Aorta	Aorta
26	chr1:173394800-173398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:173394800-173400600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:173395200-173398600	Weak transcription	A549	lung
29	chr1:173395400-173398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:173395400-173398600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:173395400-173398800	Weak transcription	Primary T cells from cord blood	blood
32	chr1:173395600-173398600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:173395600-173398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:173396200-173398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:173396200-173398600	Weak transcription	Placenta	Placenta
36	chr1:173396600-173398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:173396600-173398800	Weak transcription	Colonic Mucosa	Colon
38	chr1:173397000-173398800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:173397600-173398600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr1:173397800-173398600	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:173397800-173398600	Enhancers	Fetal Muscle Leg	muscle
42	chr1:173398000-173398600	Enhancers	Adipose Nuclei	Adipose
43	chr1:173398000-173398600	Enhancers	Fetal Heart	heart
44	chr1:173398000-173398600	Enhancers	Stomach Smooth Muscle	stomach
45	chr1:173398000-173399000	Enhancers	Fetal Stomach	stomach
46	chr1:173398000-173399600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:173398200-173398600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:173398200-173398800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr1:173398200-173398800	Weak transcription	HepG2	liver
50	chr1:173398400-173398600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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