Variant report

Variant	rs11634685
Chromosome Location	chr15:74599333-74599334
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74419514..74421455-chr15:74598626..74600426,2	MCF-7	breast:
2	chr15:74419808..74420446-chr15:74598539..74599345,2	MCF-7	breast:
3	chr15:74419530..74420527-chr15:74599297..74600836,14	MCF-7	breast:
4	chr15:74412284..74415144-chr15:74598064..74600098,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167178	Chromatin interaction
ENSG00000248540	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11072478	0.83[MEX][hapmap]
rs11631552	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856695	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905100	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs12906092	0.84[CEU][hapmap];0.83[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs12913522	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917295	0.87[CEU][hapmap]
rs1484210	0.88[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1809500	0.85[EUR][1000 genomes]
rs2277602	0.84[MEX][hapmap]
rs2279378	0.86[ASW][hapmap];0.92[CEU][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899825	0.83[JPT][hapmap]
rs2930291	0.92[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2930302	0.83[MEX][hapmap]
rs2959004	0.84[MEX][hapmap]
rs2959008	0.83[MEX][hapmap]
rs2959011	0.92[MEX][hapmap]
rs351184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351189	0.81[EUR][1000 genomes]
rs397074	0.87[EUR][1000 genomes]
rs413150	0.82[EUR][1000 genomes]
rs4887131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4887132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887134	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs900799	0.80[CEU][hapmap]
rs900801	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11634685	SEMA7A	cis	cerebellum	SCAN
rs11634685	RPLP1	cis	parietal	SCAN
rs11634685	CYP1A1	cis	cerebellum	SCAN
rs11634685	ITGA11	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74584200-74607400	Weak transcription	Right Atrium	heart
2	chr15:74593800-74601000	Enhancers	Fetal Brain Female	brain
3	chr15:74593800-74601800	Enhancers	Fetal Brain Male	brain
4	chr15:74594000-74602000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr15:74596600-74600400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:74596600-74606600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:74596600-74609800	Weak transcription	A549	lung
8	chr15:74597800-74599800	Weak transcription	Brain Germinal Matrix	brain
9	chr15:74597800-74600800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:74598200-74601400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:74598200-74602000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:74598400-74599400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr15:74598400-74601400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr15:74598400-74601800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:74598600-74601200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:74598600-74601800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:74598800-74600000	Enhancers	HMEC	breast
18	chr15:74598800-74600600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:74599000-74599400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:74599000-74599600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr15:74599000-74599600	Bivalent Enhancer	Fetal Stomach	stomach
22	chr15:74599000-74600200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr15:74599000-74600400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr15:74599000-74600400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:74599000-74600800	Enhancers	NH-A	brain
26	chr15:74599000-74601200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr15:74599000-74601200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr15:74599000-74601200	Bivalent Enhancer	Fetal Intestine Small	intestine
29	chr15:74599000-74601200	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr15:74599000-74601400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr15:74599000-74601800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr15:74599200-74599600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:74599200-74599800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr15:74599200-74599800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:74599200-74599800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:74599200-74599800	Bivalent Enhancer	NHEK	skin
37	chr15:74599200-74600000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:74599200-74601600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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