Variant report

Variant	rs873615
Chromosome Location	chr11:36449540-36449541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr11:36449462-36449689	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr11:36449464-36449775	U87	brain:	n/a	n/a
3	FOS	chr11:36449521-36449715	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr11:36449444-36449775	U87	brain:	n/a	n/a
5	MYC	chr11:36449482-36449706	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000255060	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10836555	0.82[TSI][hapmap]
rs4756315	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6484855	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7107720	0.88[ASW][hapmap];0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7107829	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7117655	0.86[TSI][hapmap]
rs746761	0.96[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs751926	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751927	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs873615	CD59	cis	cerebellum	SCAN
rs873615	PAMR1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36400200-36475400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:36413000-36471000	Weak transcription	Aorta	Aorta
3	chr11:36414800-36475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:36420400-36453200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:36431200-36453200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:36432000-36467800	Weak transcription	Esophagus	oesophagus
7	chr11:36432600-36452200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:36433400-36452600	Weak transcription	Left Ventricle	heart
9	chr11:36433800-36471400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:36435200-36453400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:36435200-36463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:36438000-36450200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:36440800-36452200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:36442200-36451800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:36442600-36451200	Weak transcription	NHEK	skin
16	chr11:36442600-36462200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:36443000-36453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:36443600-36451400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:36443600-36451800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:36443600-36452600	Weak transcription	NHDF-Ad	bronchial
21	chr11:36443600-36453200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:36443800-36450200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:36443800-36457400	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:36444000-36471400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:36444200-36471400	Weak transcription	Small Intestine	intestine
26	chr11:36444400-36453000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:36445400-36449600	Enhancers	Fetal Muscle Leg	muscle
28	chr11:36445600-36452400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:36446800-36449600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:36446800-36449800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr11:36447000-36449600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr11:36447000-36449800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:36447000-36450400	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr11:36447200-36449600	Strong transcription	Colonic Mucosa	Colon
35	chr11:36447200-36450000	Enhancers	Brain Hippocampus Middle	brain
36	chr11:36447400-36449800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:36447600-36450400	Enhancers	Brain Substantia Nigra	brain
38	chr11:36447600-36451200	Weak transcription	Psoas Muscle	Psoas
39	chr11:36447600-36453000	Weak transcription	Hela-S3	cervix
40	chr11:36447600-36471000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:36447800-36451000	Strong transcription	Fetal Intestine Large	intestine
42	chr11:36447800-36451200	Weak transcription	HSMM	muscle
43	chr11:36448200-36449800	Enhancers	Osteobl	bone
44	chr11:36448400-36449800	Enhancers	Lung	lung
45	chr11:36448400-36450200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:36448400-36450200	Enhancers	Brain Cingulate Gyrus	brain
47	chr11:36448400-36452600	Weak transcription	HSMMtube	muscle
48	chr11:36448400-36463800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr11:36448400-36470600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:36448600-36449600	Strong transcription	Rectal Smooth Muscle	rectum

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