Variant report

Variant	rs6703387
Chromosome Location	chr1:114341332-114341333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114332261..114335677-chr1:114340949..114344053,3	K562	blood:
2	chr1:114339066..114343299-chr1:114345760..114348770,4	K562	blood:
3	chr1:114328870..114331856-chr1:114340640..114342248,2	K562	blood:
4	chr1:114333134..114336494-chr1:114338300..114342659,7	MCF-7	breast:
5	chr1:114335490..114338068-chr1:114340379..114342249,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10127930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10489936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1080307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1217384	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1217394	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs12723023	0.82[EUR][1000 genomes]
rs12729708	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12730735	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12731010	0.85[EUR][1000 genomes]
rs12734625	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12735104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739970	0.82[EUR][1000 genomes]
rs12746609	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12748727	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12752932	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12753075	0.84[EUR][1000 genomes]
rs12753351	0.88[EUR][1000 genomes]
rs12758546	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12760457	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[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13374352	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1539438	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs17274550	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17274620	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17274634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs17359302	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17462614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17509390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2040040	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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2359174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2476601	1.00[LWK][hapmap]
rs34042871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34341173	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34649199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34698891	0.89[EUR][1000 genomes]
rs34857922	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34877889	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35320278	0.88[EUR][1000 genomes]
rs35383900	0.88[EUR][1000 genomes]
rs35836713	0.88[EUR][1000 genomes]
rs36115604	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3748003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3752953	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs3761931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs3789595	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3789599	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789607	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[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61817579	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61817586	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61817617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819423	0.84[EUR][1000 genomes]
rs61819424	0.81[EUR][1000 genomes]
rs61820162	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674848	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];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7533391	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533605	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549685	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7555354	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9803891	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6703387	CD58	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
4	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:114327400-114341600	Weak transcription	Colonic Mucosa	Colon
7	chr1:114327400-114348800	Weak transcription	Spleen	Spleen
8	chr1:114327400-114351200	Weak transcription	Fetal Brain Male	brain
9	chr1:114329200-114341600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:114329200-114345800	Weak transcription	Small Intestine	intestine
11	chr1:114329200-114353600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:114332000-114346400	Weak transcription	Gastric	stomach
13	chr1:114332000-114346800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:114332400-114341600	Weak transcription	Right Ventricle	heart
15	chr1:114332400-114346600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:114332400-114347200	Weak transcription	Right Atrium	heart
17	chr1:114332400-114353400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:114335000-114342000	Strong transcription	K562	blood
19	chr1:114335400-114341400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:114335400-114341400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:114336000-114351200	Weak transcription	Fetal Brain Female	brain
22	chr1:114336200-114351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:114336200-114351200	Weak transcription	HMEC	breast
24	chr1:114336400-114347000	Weak transcription	NHLF	lung
25	chr1:114336600-114347000	Weak transcription	NHEK	skin
26	chr1:114336600-114347200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:114336600-114347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:114336800-114343600	Weak transcription	Pancreas	Pancrea
29	chr1:114336800-114346400	Weak transcription	Psoas Muscle	Psoas
30	chr1:114336800-114348400	Weak transcription	Fetal Stomach	stomach
31	chr1:114336800-114349400	Weak transcription	Lung	lung
32	chr1:114337000-114341400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:114337200-114352600	Weak transcription	Fetal Kidney	kidney
34	chr1:114337600-114341400	Weak transcription	Brain Anterior Caudate	brain
35	chr1:114337600-114341600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:114337600-114346000	Weak transcription	Stomach Mucosa	stomach
37	chr1:114337600-114347000	Weak transcription	Osteobl	bone
38	chr1:114338000-114341600	Weak transcription	Fetal Heart	heart
39	chr1:114338000-114347000	Weak transcription	Fetal Intestine Small	intestine
40	chr1:114338200-114341800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:114338600-114347000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:114339000-114346800	Weak transcription	HUVEC	blood vessel
43	chr1:114339800-114343200	Weak transcription	HSMMtube	muscle
44	chr1:114340000-114351800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:114340400-114341600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:114340400-114342000	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr1:114340400-114345400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:114340400-114347000	Weak transcription	HSMM	muscle
49	chr1:114340400-114347000	Weak transcription	NHDF-Ad	bronchial
50	chr1:114340400-114352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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