Variant report

Variant	rs3934577
Chromosome Location	chr1:173398310-173398311
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10737300	0.82[ASN][1000 genomes]
rs10912614	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs11799616	0.82[ASN][1000 genomes]
rs11800778	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11809166	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11811598	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12075952	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12562415	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34619706	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4554754	0.82[ASN][1000 genomes]
rs4916354	0.81[ASN][1000 genomes]
rs55741047	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55816799	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57231379	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57262055	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59568490	0.94[AFR][1000 genomes]
rs59834293	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60302114	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60969203	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61061894	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61261546	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678064	0.93[CHB][hapmap];0.82[CHD][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs6700269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6700499	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72726915	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72726936	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72726946	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72726948	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72726949	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74126390	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7529959	0.98[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7534736	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555324	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3934577		cis	Lymphoblastoid	GTEx
rs3934577	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 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	chr1:173378400-173398400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:173379000-173398400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:173380200-173398400	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:173380200-173398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:173380200-173398600	Weak transcription	Psoas Muscle	Psoas
10	chr1:173380400-173398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173380400-173398600	Weak transcription	Thymus	Thymus
12	chr1:173380400-173398800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:173383000-173398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:173385600-173398600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:173385600-173398600	Weak transcription	Spleen	Spleen
16	chr1:173387600-173429000	Weak transcription	Lung	lung
17	chr1:173387800-173398400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:173387800-173398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:173388000-173398400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:173388000-173398400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:173388000-173398600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:173389600-173398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:173389600-173398400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:173389600-173398400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:173389600-173398400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:173389600-173398400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:173389600-173398400	Weak transcription	NH-A	brain
28	chr1:173389600-173398600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:173389600-173398600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:173389600-173398600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:173389600-173398600	Weak transcription	Left Ventricle	heart
32	chr1:173389600-173399200	Weak transcription	Pancreas	Pancrea
33	chr1:173389600-173400600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:173389800-173398400	Weak transcription	Fetal Lung	lung
35	chr1:173390000-173398400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:173390000-173398400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:173390000-173398400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:173390000-173398600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:173390000-173398600	Weak transcription	HUVEC	blood vessel
40	chr1:173391800-173398400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:173391800-173398400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:173391800-173429000	Weak transcription	Ovary	ovary
43	chr1:173392000-173398400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:173392000-173398600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:173392000-173398600	Weak transcription	Aorta	Aorta
46	chr1:173392800-173398400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:173392800-173398400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:173394600-173398400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:173394800-173398400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:173394800-173398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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