Variant report

Variant	rs11604141
Chromosome Location	chr11:85499290-85499291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85498273..85503366-chr11:85519717..85522661,4	MCF-7	breast:
2	chr11:85491140..85492854-chr11:85498576..85500721,2	MCF-7	breast:
3	chr11:85495095..85500419-chr11:85536956..85541120,6	MCF-7	breast:
4	chr11:85498616..85500121-chr11:85521754..85523993,2	MCF-7	breast:
5	chr11:85498596..85501335-chr11:85503277..85506265,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11234410	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151152	0.97[ASN][1000 genomes]
rs11604178	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606818	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12792050	0.97[ASN][1000 genomes]
rs1445497	0.86[CEU][hapmap]
rs1445513	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817179	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.89[ASN][1000 genomes]
rs188311	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2467059	0.81[JPT][hapmap]
rs290175	0.81[JPT][hapmap]
rs290177	0.81[JPT][hapmap]
rs290186	0.81[JPT][hapmap]
rs290194	0.81[JPT][hapmap]
rs290196	0.81[JPT][hapmap]
rs290199	0.81[JPT][hapmap]
rs3862785	0.89[CHB][hapmap]
rs493673	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4943925	0.80[CHB][hapmap]
rs4944538	0.86[CEU][hapmap]
rs4944539	0.84[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs497158	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs510948	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs520629	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521764	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537266	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs537604	0.87[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs543995	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558377	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs565494	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56579	0.81[JPT][hapmap]
rs573766	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs578324	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs583122	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs592380	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs592712	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs609012	0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs613973	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs61907272	0.90[ASN][1000 genomes]
rs630613	0.86[CEU][hapmap]
rs631104	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs639688	0.87[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs644558	0.97[ASN][1000 genomes]
rs650036	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs650970	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs653559	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs666176	0.87[ASN][1000 genomes]
rs667080	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs681044	0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs683903	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688741	0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7103790	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription 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	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11604141	RAB38	cis	cerebellum	SCAN
rs11604141	GRM5	cis	parietal	SCAN
rs11604141	SYTL2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85491000-85499600	Enhancers	Stomach Mucosa	stomach
2	chr11:85491800-85517800	Weak transcription	NHLF	lung
3	chr11:85492200-85502800	Weak transcription	Small Intestine	intestine
4	chr11:85493000-85499400	Weak transcription	HMEC	breast
5	chr11:85493400-85501200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:85493400-85502400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:85494000-85502400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:85496400-85510600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:85497200-85500000	Enhancers	Fetal Intestine Large	intestine
10	chr11:85497600-85500000	Enhancers	Fetal Intestine Small	intestine
11	chr11:85498000-85499800	Enhancers	Hela-S3	cervix
12	chr11:85498000-85499800	Enhancers	HSMM	muscle
13	chr11:85498200-85499400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr11:85498200-85500000	Enhancers	HSMMtube	muscle
15	chr11:85498400-85499400	Enhancers	Primary T cells from cord blood	blood
16	chr11:85498400-85499800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr11:85498600-85499400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:85498800-85499600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr11:85498800-85499600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr11:85498800-85499600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr11:85498800-85499800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr11:85498800-85499800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:85498800-85499800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:85498800-85499800	Enhancers	HepG2	liver
25	chr11:85498800-85503200	Weak transcription	Colonic Mucosa	Colon
26	chr11:85499000-85499400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:85499000-85499600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr11:85499000-85499600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr11:85499000-85499800	Enhancers	Fetal Heart	heart
30	chr11:85499000-85499800	Enhancers	NHEK	skin
31	chr11:85499000-85500000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:85499000-85500000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:85499200-85499400	Weak transcription	NHDF-Ad	bronchial
34	chr11:85499200-85499600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr11:85499200-85499800	Flanking Active TSS	A549	lung
36	chr11:85499200-85510400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr11:85499200-85517200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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