Variant report

Variant	rs11227147
Chromosome Location	chr11:64958006-64958007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64956427..64958722-chr11:64980745..64983339,2	K562	blood:
2	chr11:64901296..64904246-chr11:64957892..64962148,4	MCF-7	breast:
3	chr11:64957988..64959551-chr11:64991502..64993463,2	K562	blood:
4	chr11:64877165..64880640-chr11:64955591..64959412,3	K562	blood:
5	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
6	chr11:64951297..64953608-chr11:64956133..64959941,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149806	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000197847	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000174276	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11227153	0.80[JPT][hapmap]
rs11227154	0.82[JPT][hapmap]
rs1195963	0.85[CEU][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1195964	0.85[CEU][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12279142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs171193	0.84[EUR][1000 genomes]
rs17884154	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2089921	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271446	0.82[JPT][hapmap]
rs2271449	0.82[JPT][hapmap]
rs239253	0.82[GIH][hapmap]
rs239256	0.82[GIH][hapmap]
rs2904978	0.83[MEX][hapmap]
rs4492832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542380	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs580734	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs600135	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678296	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678343	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7102307	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7116156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7116556	0.84[AMR][1000 genomes];0.81[EUR][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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11227147	TM7SF2	cis	cerebellum	SCAN
rs11227147	POLA2	cis	cerebellum	SCAN
rs11227147	RPS6KB2	cis	cerebellum	SCAN
rs11227147	BBS1	cis	cerebellum	SCAN
rs11227147	CARNS1	cis	parietal	SCAN
rs11227147	POLA2	cis	parietal	SCAN
rs11227147	GAL3ST3	cis	cerebellum	SCAN
rs11227147	DPP3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64950400-64973200	Weak transcription	Fetal Kidney	kidney
2	chr11:64950600-64992400	Weak transcription	Right Atrium	heart
3	chr11:64951000-64959000	Strong transcription	Thymus	Thymus
4	chr11:64951000-64959200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:64951000-64973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:64951000-64976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:64951200-64958400	Strong transcription	NHLF	lung
8	chr11:64951200-64958800	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:64951200-64959800	Strong transcription	Primary T cells from cord blood	blood
10	chr11:64951200-64961800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:64951200-64962800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:64951200-64963000	Strong transcription	Liver	Liver
13	chr11:64951200-64963000	Strong transcription	Fetal Stomach	stomach
14	chr11:64951200-64963200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:64951200-64963600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:64951200-64968400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:64951200-64976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:64951400-64958800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr11:64951400-64959200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:64951400-64960000	Strong transcription	Adipose Nuclei	Adipose
21	chr11:64951400-64963400	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:64951400-64968000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:64951400-64979200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:64951600-64976400	Weak transcription	Fetal Brain Male	brain
25	chr11:64951600-64979600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:64951800-64958200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:64951800-64958200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:64951800-64958400	Strong transcription	Lung	lung
29	chr11:64951800-64958400	Strong transcription	Spleen	Spleen
30	chr11:64951800-64958600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:64951800-64958800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:64951800-64959000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:64951800-64963200	Strong transcription	Fetal Intestine Large	intestine
34	chr11:64951800-64968800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr11:64951800-64969000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:64952000-64958600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:64952000-64962200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:64952200-64960000	Strong transcription	Primary B cells from cord blood	blood
39	chr11:64952200-64960000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr11:64952200-64960200	Strong transcription	Fetal Thymus	thymus
41	chr11:64952200-64960400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr11:64952200-64961600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:64952400-64958200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:64952400-64958400	Strong transcription	Pancreas	Pancrea
45	chr11:64952400-64960000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:64952400-64962800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:64952400-64963000	Strong transcription	Fetal Intestine Small	intestine
48	chr11:64952400-64967400	Strong transcription	Placenta	Placenta
49	chr11:64952400-64972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:64952400-64980200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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