Variant report

Variant	rs6676190
Chromosome Location	chr1:151079317-151079318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151079279..151081159-chr1:151117382..151120022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10749659	0.87[ASN][1000 genomes]
rs10788797	0.89[CHB][hapmap]
rs10788798	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10788800	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888404	0.85[EUR][1000 genomes]
rs10888405	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204772	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11204777	1.00[JPT][hapmap]
rs11204779	0.90[ASN][1000 genomes]
rs11204780	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11204782	1.00[JPT][hapmap]
rs11807526	1.00[JPT][hapmap]
rs12039522	0.84[EUR][1000 genomes]
rs12087892	1.00[JPT][hapmap]
rs12134957	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12569193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs1524773	1.00[JPT][hapmap]
rs15740	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs2067606	1.00[JPT][hapmap]
rs2091219	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap]
rs2140709	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2864700	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs2902810	0.83[CHD][hapmap]
rs3738481	1.00[JPT][hapmap]
rs3806386	0.83[CHD][hapmap]
rs4357530	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360524	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4512652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4970936	0.85[ASN][1000 genomes]
rs4970941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970991	0.82[CHB][hapmap]
rs4970993	1.00[JPT][hapmap]
rs4970997	0.88[ASN][1000 genomes]
rs4970998	0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4971002	0.81[ASN][1000 genomes]
rs4971005	0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4971006	0.81[ASN][1000 genomes]
rs4971007	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4971008	1.00[JPT][hapmap]
rs61819219	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587552	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs6587553	0.83[CHD][hapmap]
rs6587557	0.86[JPT][hapmap]
rs6656450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674970	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs6691701	0.82[CHB][hapmap]
rs6697617	0.87[ASN][1000 genomes]
rs6702344	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7414477	0.88[EUR][1000 genomes]
rs7522608	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7523731	1.00[JPT][hapmap]
rs7536234	0.89[EUR][1000 genomes]
rs7546304	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554936	0.96[CEU][hapmap];1.00[JPT][hapmap]

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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872421	chr1:151055670-151098077	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6676190	GABPB2	cis	cerebellum	SCAN
rs6676190	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs6676190	PEX11B	cis	parietal	SCAN
rs6676190	CDC42SE1	cis	Lymphoblastoid	GTEx
rs6676190	BNIPL	cis	lung	GTEx
rs6676190	CDC42SE1	cis	lymphoblastoid	seeQTL
rs6676190	PRPF3	cis	cerebellum	SCAN
rs6676190	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs6676190	PRPF3	cis	parietal	SCAN
rs6676190	CDC42SE1	cis	parietal	SCAN
rs6676190	LYSMD1	cis	parietal	SCAN
rs6676190	ZNF687	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
2	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
3	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
4	chr1:151044400-151079600	Weak transcription	Lung	lung
5	chr1:151044400-151090200	Weak transcription	Gastric	stomach
6	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
7	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
8	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:151044800-151079600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:151044800-151080200	Weak transcription	Fetal Brain Female	brain
13	chr1:151044800-151089400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:151045000-151079400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:151045000-151080000	Weak transcription	Brain Angular Gyrus	brain
17	chr1:151045000-151080400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:151045200-151081000	Weak transcription	Placenta	Placenta
19	chr1:151047200-151090400	Weak transcription	Dnd41	blood
20	chr1:151047400-151090400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:151047800-151079600	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:151047800-151089200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:151052200-151103000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:151056200-151079600	Weak transcription	Primary B cells from cord blood	blood
25	chr1:151060600-151090200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:151061800-151090400	Weak transcription	Fetal Kidney	kidney
27	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:151062000-151079400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:151062200-151088800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:151063200-151080800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:151063400-151079600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:151064200-151103400	Weak transcription	Colonic Mucosa	Colon
33	chr1:151064400-151079600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:151067000-151103400	Weak transcription	Fetal Brain Male	brain
35	chr1:151067800-151079400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:151068000-151079400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:151068400-151090400	Weak transcription	Pancreas	Pancrea
38	chr1:151068600-151079600	Weak transcription	Brain Germinal Matrix	brain
39	chr1:151070200-151079400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:151070200-151079600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:151070600-151079400	Weak transcription	Hela-S3	cervix
42	chr1:151071000-151079600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:151071000-151079600	Weak transcription	Fetal Intestine Large	intestine
44	chr1:151071000-151087000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:151071200-151079400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:151071200-151079600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:151071200-151080800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:151071400-151090400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:151072400-151091400	Weak transcription	Fetal Lung	lung
50	chr1:151074000-151101000	Weak transcription	Fetal Heart	heart

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