Variant report

Variant	rs2040040
Chromosome Location	chr1:114331645-114331646
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114328514..114333064-chr1:114341407..114344891,4	MCF-7	breast:
2	chr1:114327966..114331682-chr1:114351317..114354646,4	K562	blood:
3	chr1:114330964..114333642-chr1:114352600..114356099,4	MCF-7	breast:
4	chr1:114330207..114332074-chr20:52046883..52049552,2	MCF-7	breast:
5	chr1:114328870..114331856-chr1:114340640..114342248,2	K562	blood:
6	chr1:114317996..114324872-chr1:114329159..114335059,8	K562	blood:
7	chr1:114324961..114329121-chr1:114330799..114335017,4	K562	blood:
8	chr1:114329880..114331707-chr1:114332071..114335621,3	K562	blood:
9	chr1:114300369..114304459-chr1:114329626..114333036,4	MCF-7	breast:
10	chr1:114330552..114332424-chr1:114422086..114424136,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000081019	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000231128	Chromatin interaction

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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[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];0.90[EUR][1000 genomes]
rs1217394	1.00[ASW][hapmap]
rs12723023	0.84[EUR][1000 genomes]
rs12729708	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730735	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12731010	0.86[EUR][1000 genomes]
rs12734625	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12735104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12739970	0.84[EUR][1000 genomes]
rs12746609	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12748727	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12752932	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12753075	0.85[EUR][1000 genomes]
rs12753351	0.89[EUR][1000 genomes]
rs12758546	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374352	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1539438	1.00[ASW][hapmap]
rs17274550	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17274620	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[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];0.89[EUR][1000 genomes]
rs17359302	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17462614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][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];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[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];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2476601	1.00[LWK][hapmap]
rs34042871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34341173	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34649199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34698891	0.90[EUR][1000 genomes]
rs34857922	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34877889	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35320278	0.89[EUR][1000 genomes]
rs35383900	0.89[EUR][1000 genomes]
rs35836713	0.89[EUR][1000 genomes]
rs36115604	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.89[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];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[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];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3789595	0.82[AMR][1000 genomes];0.89[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];0.91[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817579	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61817586	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61817617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61819423	0.85[EUR][1000 genomes]
rs61819424	0.82[EUR][1000 genomes]
rs61820162	0.82[AMR][1000 genomes];0.89[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];1.00[EUR][1000 genomes];1.00[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];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6703387	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]
rs7533391	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7533605	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549685	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7555354	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9803891	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[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
rs2040040	CD58	cis	cerebellum	SCAN

Chromatin state (count:120 , 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	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney
5	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
6	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:114320000-114336200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:114320000-114340000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:114320200-114337200	Weak transcription	Placenta	Placenta
11	chr1:114320400-114337200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:114326600-114335000	Weak transcription	Fetal Stomach	stomach
13	chr1:114326600-114335200	Weak transcription	HMEC	breast
14	chr1:114326600-114337800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:114326800-114335200	Weak transcription	HUVEC	blood vessel
16	chr1:114326800-114335800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:114326800-114335800	Weak transcription	NH-A	brain
18	chr1:114326800-114338600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:114326800-114340000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:114327000-114335000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:114327000-114335200	Weak transcription	NHDF-Ad	bronchial
22	chr1:114327000-114336000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:114327000-114337000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:114327200-114331800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:114327200-114332000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:114327200-114333200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:114327200-114334800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:114327200-114337400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:114327400-114331800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:114327400-114331800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:114327400-114331800	Weak transcription	Left Ventricle	heart
32	chr1:114327400-114331800	Weak transcription	Lung	lung
33	chr1:114327400-114331800	Weak transcription	Ovary	ovary
34	chr1:114327400-114331800	Weak transcription	Right Atrium	heart
35	chr1:114327400-114331800	Weak transcription	Right Ventricle	heart
36	chr1:114327400-114332000	Weak transcription	HSMM	muscle
37	chr1:114327400-114332000	Weak transcription	NHEK	skin
38	chr1:114327400-114335000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:114327400-114335200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:114327400-114335400	Weak transcription	Fetal Brain Female	brain
41	chr1:114327400-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:114327400-114336400	Weak transcription	Thymus	Thymus
43	chr1:114327400-114336600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:114327400-114336800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:114327400-114337600	Weak transcription	Adipose Nuclei	Adipose
46	chr1:114327400-114337600	Weak transcription	Fetal Lung	lung
47	chr1:114327400-114339200	Weak transcription	HSMMtube	muscle
48	chr1:114327400-114341600	Weak transcription	Colonic Mucosa	Colon
49	chr1:114327400-114348800	Weak transcription	Spleen	Spleen
50	chr1:114327400-114351200	Weak transcription	Fetal Brain Male	brain

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