Variant report

Variant	rs2043675
Chromosome Location	chr2:85769975-85769976
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85645994..85650779-chr2:85769890..85775374,14	MCF-7	breast:
2	chr2:85616263..85635094-chr2:85763849..85770697,56	MCF-7	breast:
3	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
4	chr2:85729372..85732165-chr2:85769657..85772288,2	MCF-7	breast:
5	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
6	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
7	chr2:85716297..85718837-chr2:85769443..85771009,2	K562	blood:
8	chr2:85764346..85769986-chr2:85836202..85840842,10	MCF-7	breast:
9	chr2:85767293..85770194-chr2:85815993..85818775,2	MCF-7	breast:
10	chr2:85658029..85667242-chr2:85763719..85770665,19	MCF-7	breast:
11	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
12	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:
13	chr2:85617430..85626766-chr2:85763113..85771250,22	MCF-7	breast:
14	chr2:85766117..85770203-chr2:85837145..85839440,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000199936	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000252293	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1009	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1010	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs10179195	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10180770	0.84[JPT][hapmap]
rs10182351	0.84[JPT][hapmap]
rs10187424	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs10198569	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs10206961	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1058588	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1078004	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs11126995	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1124836	0.84[JPT][hapmap]
rs11895341	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895399	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895401	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473819	0.80[ASN][1000 genomes]
rs12615553	0.86[ASN][1000 genomes]
rs13383605	0.84[JPT][hapmap]
rs1348818	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs14242	0.90[JPT][hapmap]
rs1446669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561198	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1562322	0.90[JPT][hapmap]
rs17026396	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs2028898	0.93[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028900	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2044474	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2044475	0.82[TSI][hapmap]
rs2232745	0.84[JPT][hapmap]
rs2232747	0.84[JPT][hapmap]
rs2232750	0.84[JPT][hapmap]
rs2289972	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304564	0.84[JPT][hapmap]
rs2592551	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731828	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755008	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755011	0.90[JPT][hapmap]
rs3755015	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3770098	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3821020	0.84[JPT][hapmap]
rs3827550	0.84[JPT][hapmap]
rs55692129	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56819945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58307667	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs58644336	0.89[ASN][1000 genomes]
rs58768785	0.86[ASN][1000 genomes]
rs60012532	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60788310	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6547621	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6547622	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6643	0.84[JPT][hapmap]
rs6705971	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs6722691	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731700	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6735663	0.90[ASN][1000 genomes]
rs6738645	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6743051	0.84[JPT][hapmap]
rs6757263	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs67988001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699664	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72643495	0.94[ASN][1000 genomes]
rs73943244	0.85[ASN][1000 genomes]
rs7568458	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7579147	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7579665	0.82[TSI][hapmap]
rs7593969	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605975	0.80[ASN][1000 genomes]
rs7608074	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs762684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2043675	RNF181	cis	parietal	SCAN
rs2043675	VAMP8	cis	lymphoblastoid	seeQTL
rs2043675	GGCX	cis	parietal	SCAN
rs2043675	MAT2A	cis	cerebellum	SCAN
rs2043675	VAMP8	cis	parietal	SCAN
rs2043675	GGCX	cis	cerebellum	SCAN
rs2043675	VAMP8	cis	lesional skin	skin_eQTL
rs2043675	VAMP8	cis	uninvolved skin	skin_eQTL
rs2043675	VAMP8	cis	multi-tissue	Pritchard
rs2043675	RNF103	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85766400-85770200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr2:85766400-85770600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
3	chr2:85766400-85770600	Transcr. at gene 5' and 3'	NHLF	lung
4	chr2:85766600-85770800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:85766800-85770000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:85766800-85770200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr2:85766800-85770600	Transcr. at gene 5' and 3'	A549	lung
8	chr2:85767000-85770000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
9	chr2:85767000-85770000	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
10	chr2:85767000-85770200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
11	chr2:85767000-85770200	Transcr. at gene 5' and 3'	NHEK	skin
12	chr2:85767000-85770400	Transcr. at gene 5' and 3'	K562	blood
13	chr2:85767000-85770600	Transcr. at gene 5' and 3'	HSMM	muscle
14	chr2:85767000-85771800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:85767200-85770000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:85767200-85770200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr2:85767200-85770400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
18	chr2:85767200-85770600	Transcr. at gene 5' and 3'	Hela-S3	cervix
19	chr2:85767400-85770200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:85767400-85770200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:85767400-85770600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
22	chr2:85767600-85770200	Transcr. at gene 5' and 3'	HMEC	breast
23	chr2:85767600-85770200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
24	chr2:85767800-85770400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:85767800-85771000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
26	chr2:85768200-85770000	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
27	chr2:85768200-85770200	Transcr. at gene 5' and 3'	HSMMtube	muscle
28	chr2:85768400-85770000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
29	chr2:85768400-85770200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
30	chr2:85768400-85770200	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:85768400-85770400	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
32	chr2:85768400-85771400	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr2:85768400-85773800	Strong transcription	Lung	lung
34	chr2:85768400-85774200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:85768400-85774800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:85768400-85774800	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr2:85768400-85777000	Strong transcription	Placenta	Placenta
38	chr2:85768400-85778000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:85768600-85770400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:85768600-85770400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr2:85768600-85770600	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:85768600-85773200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:85768600-85773200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:85768600-85774600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:85768600-85779000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:85768600-85786200	Strong transcription	Fetal Thymus	thymus
48	chr2:85768800-85770000	Genic enhancers	Liver	Liver
49	chr2:85768800-85770200	Genic enhancers	Primary hematopoietic stem cells	blood
50	chr2:85768800-85770200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood

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