Variant report

Variant	rs11633101
Chromosome Location	chr15:74537753-74537754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74531319..74532959-chr15:74536975..74539724,2	MCF-7	breast:
2	chr15:74530832..74532774-chr15:74536942..74538994,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11629834	0.80[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11633321	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638601	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11639316	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12898529	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904523	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905224	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905234	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905362	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913344	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913651	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564784	0.92[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs168432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189497	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351153	0.89[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351159	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs351174	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351175	0.81[JPT][hapmap]
rs351180	0.91[ASN][1000 genomes]
rs351181	0.91[ASN][1000 genomes]
rs3848162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67882706	0.85[ASN][1000 genomes]
rs901128	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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
3	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv904349	chr15:74500105-74542686	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11633101	SCAMP2	cis	cerebellum	SCAN
rs11633101	CORO2B	cis	parietal	SCAN
rs11633101	CELF6	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74531600-74538400	Enhancers	Spleen	Spleen
2	chr15:74532800-74543200	Weak transcription	Psoas Muscle	Psoas
3	chr15:74535400-74537800	Weak transcription	HMEC	breast
4	chr15:74535400-74542200	Weak transcription	Right Atrium	heart
5	chr15:74535600-74537800	Weak transcription	Fetal Heart	heart
6	chr15:74535600-74537800	Weak transcription	Gastric	stomach
7	chr15:74535600-74537800	Weak transcription	Left Ventricle	heart
8	chr15:74535600-74542200	Weak transcription	HSMMtube	muscle
9	chr15:74535600-74543800	Weak transcription	Right Ventricle	heart
10	chr15:74536400-74539200	Enhancers	Fetal Brain Male	brain
11	chr15:74536600-74537800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr15:74536800-74538400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr15:74536800-74538400	Enhancers	Fetal Thymus	thymus
14	chr15:74537000-74537800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr15:74537000-74537800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr15:74537000-74537800	Enhancers	Thymus	Thymus
17	chr15:74537000-74538400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr15:74537000-74538400	Bivalent Enhancer	Fetal Stomach	stomach
19	chr15:74537000-74538600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:74537200-74537800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:74537200-74537800	Enhancers	Fetal Intestine Small	intestine
22	chr15:74537200-74537800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr15:74537200-74538000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:74537200-74538000	Enhancers	Lung	lung
25	chr15:74537200-74538400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:74537200-74538400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr15:74537200-74538400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:74537200-74538400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr15:74537200-74538600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr15:74537400-74537800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr15:74537400-74537800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
32	chr15:74537400-74537800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr15:74537400-74537800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
34	chr15:74537400-74537800	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr15:74537400-74537800	Flanking Active TSS	Fetal Brain Female	brain
36	chr15:74537400-74537800	Enhancers	HSMM	muscle
37	chr15:74537400-74538000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:74537400-74538000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:74537400-74538000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr15:74537400-74538000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:74537400-74538000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr15:74537400-74538000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:74537400-74538000	Enhancers	Pancreas	Pancrea
44	chr15:74537400-74538000	Enhancers	Stomach Mucosa	stomach
45	chr15:74537400-74538200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr15:74537400-74538200	Enhancers	Brain Angular Gyrus	brain
47	chr15:74537400-74538400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:74537400-74538400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:74537400-74538400	Enhancers	Brain Substantia Nigra	brain
50	chr15:74537400-74538400	Bivalent Enhancer	Fetal Intestine Large	intestine

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