Variant report

Variant	rs11972278
Chromosome Location	chr7:33431364-33431365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1008582	0.95[CHB][hapmap]
rs10225698	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10230133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10247780	0.83[ASN][1000 genomes]
rs10250045	0.85[CHB][hapmap]
rs10256994	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10268074	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs10279081	0.85[CHB][hapmap]
rs1030029	0.80[CHD][hapmap]
rs10464226	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951383	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs12155105	0.86[CHB][hapmap]
rs12537278	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs12665869	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12669595	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12671191	0.85[CHB][hapmap]
rs13241465	0.84[CHB][hapmap];0.90[CHD][hapmap]
rs1345277	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1345308	0.80[CHB][hapmap]
rs1362228	0.84[CHB][hapmap]
rs1362230	0.84[CHB][hapmap]
rs1362371	0.80[CHB][hapmap]
rs1419898	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs1419900	0.87[CHD][hapmap]
rs1419903	0.85[ASN][1000 genomes]
rs1419916	0.84[CHB][hapmap];0.90[CHD][hapmap]
rs1419918	0.84[CHB][hapmap]
rs1419919	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs1419921	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1419925	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1419927	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1419928	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1420158	0.80[CHB][hapmap]
rs1473155	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1592465	0.83[CHD][hapmap]
rs1894810	0.90[CHD][hapmap]
rs1894873	0.80[CHB][hapmap]
rs2024430	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs2041419	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2392233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2392234	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3884597	0.93[ASW][hapmap];0.89[CEU][hapmap];0.87[TSI][hapmap]
rs4141012	0.84[CHB][hapmap]
rs4236337	0.84[CHB][hapmap];0.90[CHD][hapmap]
rs4509212	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs4510745	0.84[CHB][hapmap]
rs4582453	0.90[CHD][hapmap]
rs4637716	0.95[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4720115	0.80[CHB][hapmap];0.80[CHD][hapmap]
rs4720118	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723283	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723288	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58961617	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59532834	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6462467	0.85[CHB][hapmap]
rs6462477	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462479	0.83[CHB][hapmap]
rs6958002	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964756	0.90[JPT][hapmap]
rs6967374	0.85[AMR][1000 genomes]
rs6976311	0.95[CHB][hapmap]
rs6977009	0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721533	0.80[CHD][hapmap]
rs721851	0.90[CHD][hapmap]
rs723300	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs726463	0.90[CHD][hapmap]
rs758779	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs758780	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764041	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs7778657	0.85[CHB][hapmap]
rs7779367	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7798984	0.83[ASN][1000 genomes]
rs7802888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804731	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7805192	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964707	0.80[CHD][hapmap]
rs975791	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9784973	0.86[ASW][hapmap];0.89[CEU][hapmap];0.87[TSI][hapmap]
rs986553	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606610	chr7:33218763-33486316	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv916660	chr7:33272493-33506384	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv830944	chr7:33389892-33549882	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11972278	AAA1	cis	cerebellum	SCAN
rs11972278	BBS9	cis	lymphoblastoid	seeQTL
rs11972278	BBS9	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33389000-33437400	Weak transcription	Liver	Liver
2	chr7:33403400-33437800	Weak transcription	Brain Substantia Nigra	brain
3	chr7:33404000-33433000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:33408200-33434600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:33408600-33434400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:33412200-33433200	Weak transcription	Psoas Muscle	Psoas
7	chr7:33418000-33438600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr7:33418200-33436400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:33418600-33434800	Weak transcription	Fetal Kidney	kidney
10	chr7:33419000-33436800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:33420000-33433200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:33420000-33435000	Weak transcription	Brain Anterior Caudate	brain
13	chr7:33420400-33431800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:33420400-33435000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:33420400-33436400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:33420400-33444600	Weak transcription	Left Ventricle	heart
17	chr7:33420600-33431800	Weak transcription	Aorta	Aorta
18	chr7:33420600-33433200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:33420600-33435000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:33420600-33435200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr7:33420600-33437800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:33420600-33449200	Weak transcription	Ovary	ovary
23	chr7:33420800-33432800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:33420800-33434600	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:33420800-33435000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:33420800-33435000	Weak transcription	Fetal Lung	lung
27	chr7:33420800-33437400	Weak transcription	Fetal Intestine Large	intestine
28	chr7:33420800-33437800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:33421000-33439800	Weak transcription	Fetal Stomach	stomach
30	chr7:33421000-33442600	Weak transcription	Pancreas	Pancrea
31	chr7:33422200-33452200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:33422600-33437800	Weak transcription	Brain Angular Gyrus	brain
33	chr7:33424200-33435000	Weak transcription	Primary T cells from cord blood	blood
34	chr7:33424800-33434800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:33425200-33435000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:33428200-33435200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:33428200-33436200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:33428200-33438200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:33428200-33458000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr7:33428600-33435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:33429600-33431800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr7:33429800-33433600	Weak transcription	Adipose Nuclei	Adipose

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