Variant report

Variant	rs11154621
Chromosome Location	chr6:131547341-131547342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10484763	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs11154622	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754401	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755717	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758994	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759793	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759926	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs1190794	1.00[CHB][hapmap]
rs1190799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs1190801	1.00[CHB][hapmap]
rs1190805	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[ASN][1000 genomes]
rs1190806	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs11961577	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209159	1.00[CHB][hapmap]
rs1317667	1.00[ASN][1000 genomes]
rs13195700	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200165	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205441	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206776	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570348	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1729549	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1729558	1.00[CHB][hapmap]
rs1746470	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1746471	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1746473	1.00[CHB][hapmap]
rs17573187	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17651753	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17787964	1.00[CHB][hapmap]
rs1885641	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077490	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327102	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360555	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326915	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34601891	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34699635	0.85[EUR][1000 genomes]
rs35017713	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35561719	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35673664	0.83[EUR][1000 genomes]
rs35746376	1.00[ASN][1000 genomes]
rs3777474	0.81[EUR][1000 genomes]
rs3777476	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777477	0.81[YRI][hapmap];0.96[EUR][1000 genomes]
rs3777487	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs3777489	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777493	1.00[ASN][1000 genomes]
rs3850239	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903759	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs4310080	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424112	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596509	0.99[EUR][1000 genomes]
rs55893652	0.92[ASN][1000 genomes]
rs56059672	0.92[ASN][1000 genomes]
rs66533103	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67021539	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67399092	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749375	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743894	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9483238	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492861	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs9492864	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492865	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492868	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492869	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492877	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492880	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492883	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11154621	AKAP7	cis	cerebellum	SCAN
rs11154621	AKAP7	cis	parietal	SCAN
rs11154621	VNN1	cis	cerebellum	SCAN
rs11154621	VNN3	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131506800-131551800	Weak transcription	Ovary	ovary
2	chr6:131535200-131548800	Weak transcription	Aorta	Aorta
3	chr6:131535200-131562200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:131535400-131547600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:131535400-131552400	Weak transcription	HSMM	muscle
6	chr6:131535400-131555200	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:131536000-131548600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:131536800-131548800	Weak transcription	Lung	lung
9	chr6:131543000-131571200	Weak transcription	Adipose Nuclei	Adipose
10	chr6:131544200-131549200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:131546000-131547400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:131546200-131547400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:131546600-131548600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:131546600-131552000	Weak transcription	HSMMtube	muscle
15	chr6:131546600-131554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:131546600-131565400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:131546600-131565600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:131546600-131566000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:131546800-131547400	Enhancers	Liver	Liver
20	chr6:131546800-131548200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:131547000-131547400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:131547000-131547800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr6:131547000-131547800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:131547000-131547800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:131547000-131547800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:131547000-131548000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:131547000-131548000	Weak transcription	Fetal Lung	lung
28	chr6:131547000-131548200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr6:131547000-131549000	Weak transcription	Primary T cells from cord blood	blood
30	chr6:131547200-131547400	Enhancers	Brain Anterior Caudate	brain
31	chr6:131547200-131547400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:131547200-131547400	Enhancers	Pancreas	Pancrea
33	chr6:131547200-131547600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr6:131547200-131547600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:131547200-131547800	Enhancers	H1 Cell Line	embryonic stem cell

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