Variant report

Variant	rs12192159
Chromosome Location	chr6:149767105-149767106
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149353960..149356786-chr6:149766378..149768113,2	MCF-7	breast:
2	chr6:149762143..149764363-chr6:149765543..149768268,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1001305	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155640	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs11155642	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs11155645	0.84[CEU][hapmap]
rs11155646	0.91[ASN][1000 genomes]
rs11155647	0.84[CEU][hapmap]
rs11155654	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191079	0.80[CEU][hapmap]
rs12192814	0.91[ASN][1000 genomes]
rs12195922	0.82[ASN][1000 genomes]
rs12204461	0.84[CEU][hapmap]
rs12204793	0.84[CEU][hapmap]
rs17506789	0.84[CEU][hapmap]
rs1980774	0.84[CEU][hapmap]
rs2341774	0.80[AMR][1000 genomes]
rs2341775	0.80[AMR][1000 genomes]
rs58747890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62441727	1.00[ASN][1000 genomes]
rs6911411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs6920383	0.85[CEU][hapmap]
rs6932778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7349921	0.84[CEU][hapmap]
rs763590	0.84[CEU][hapmap]
rs7741099	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747354	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs7747948	1.00[ASN][1000 genomes]
rs7762222	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896	0.84[CEU][hapmap]
rs9285520	0.84[CEU][hapmap]
rs9485385	0.91[ASN][1000 genomes]
rs9485392	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485394	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9485397	1.00[ASN][1000 genomes]
rs9498322	0.84[CEU][hapmap]
rs9498323	0.85[CEU][hapmap]
rs9498324	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs9498325	0.84[CEU][hapmap]
rs9498332	0.84[CEU][hapmap]
rs9498333	0.84[CEU][hapmap]
rs9498335	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs9498336	0.84[CEU][hapmap]
rs9498337	0.84[CEU][hapmap]
rs9498338	0.82[CEU][hapmap]
rs9498341	0.84[CEU][hapmap]
rs9498342	0.84[CEU][hapmap]
rs9498349	0.91[ASN][1000 genomes]
rs9498351	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9498352	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498353	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498354	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498355	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498356	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498358	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997682	0.84[CEU][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3406755	chr6:149763459-149768057	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3368142	chr6:149764359-149767257	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3358632	chr6:149764809-149767607	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12192159	RAET1E	cis	cerebellum	SCAN
rs12192159	LRP11	cis	parietal	SCAN
rs12192159	LRP11	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149753400-149770000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:149753600-149768400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:149753600-149769600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:149761600-149769600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:149762600-149770800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:149762800-149771000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:149763200-149770000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:149763200-149771000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:149763200-149771400	Weak transcription	Pancreas	Pancrea
10	chr6:149764600-149768600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr6:149764800-149771400	Weak transcription	Spleen	Spleen
12	chr6:149765200-149771400	Weak transcription	Brain Anterior Caudate	brain
13	chr6:149765800-149767600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:149766000-149767400	Enhancers	HSMM	muscle
15	chr6:149766000-149767600	Enhancers	HSMMtube	muscle
16	chr6:149766000-149768200	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr6:149766000-149769600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:149766000-149771400	Weak transcription	Right Atrium	heart
19	chr6:149766200-149771000	Weak transcription	GM12878-XiMat	blood
20	chr6:149766200-149771200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:149766400-149767200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:149766400-149768600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:149766600-149769800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:149766600-149773000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:149766800-149771000	Weak transcription	Fetal Heart	heart
26	chr6:149766800-149771400	Weak transcription	Left Ventricle	heart
27	chr6:149766800-149771600	Weak transcription	Lung	lung
28	chr6:149767000-149767400	Enhancers	HepG2	liver

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