Variant report

Variant	rs12277747
Chromosome Location	chr11:102281614-102281615
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	chr11:102278180..102279807-chr11:102281474..102283543,3	K562	blood:
2	chr11:102275664..102278453-chr11:102281044..102282865,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10219215	0.87[CEU][hapmap]
rs1058606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10895292	0.83[EUR][1000 genomes]
rs10895293	0.83[EUR][1000 genomes]
rs10895296	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11225235	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11225236	0.83[EUR][1000 genomes]
rs11225237	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs11225242	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11225243	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225251	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11547915	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11547916	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11601671	1.00[CEU][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs11603677	0.83[EUR][1000 genomes]
rs11604008	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs11604189	1.00[CEU][hapmap]
rs11604271	0.83[EUR][1000 genomes]
rs11605010	0.98[EUR][1000 genomes]
rs11605066	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11605133	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11605573	0.83[EUR][1000 genomes]
rs11607657	0.96[EUR][1000 genomes]
rs11607908	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12269847	0.98[EUR][1000 genomes]
rs12271457	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12271900	0.96[EUR][1000 genomes]
rs12274405	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12275185	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12275349	0.87[CEU][hapmap]
rs12277594	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs12277853	1.00[CEU][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs12279056	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs12282486	0.83[EUR][1000 genomes]
rs12283885	1.00[CEU][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs12290033	0.83[EUR][1000 genomes]
rs12291114	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12293094	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12293834	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12792649	1.00[CEU][hapmap]
rs1317775	1.00[CEU][hapmap]
rs13377311	0.88[EUR][1000 genomes]
rs17349689	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17350205	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17350590	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2567752	0.85[ASN][1000 genomes]
rs549513	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs57346058	0.98[EUR][1000 genomes]
rs57562739	0.98[EUR][1000 genomes]
rs58250524	0.83[EUR][1000 genomes]
rs60056981	0.96[EUR][1000 genomes]
rs61123589	0.94[EUR][1000 genomes]
rs61334418	0.98[EUR][1000 genomes]
rs679366	0.85[ASN][1000 genomes]
rs7104841	0.98[EUR][1000 genomes]
rs7113906	0.83[EUR][1000 genomes]
rs7114048	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv898334	chr11:102272884-102353192	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12277747	DEFB119	trans	brain	seeQTL
rs12277747	ENO3	trans	brain	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102220000-102283000	Weak transcription	Hela-S3	cervix
2	chr11:102265000-102287800	Weak transcription	Psoas Muscle	Psoas
3	chr11:102265000-102290800	Weak transcription	Small Intestine	intestine
4	chr11:102272800-102282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:102273000-102282000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:102273000-102288000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:102273000-102302400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:102273200-102289800	Weak transcription	NHEK	skin
9	chr11:102273200-102292400	Weak transcription	HUVEC	blood vessel
10	chr11:102273200-102300800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:102274200-102282800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:102274400-102289600	Weak transcription	HMEC	breast
13	chr11:102274400-102294000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:102275000-102290600	Weak transcription	Fetal Intestine Large	intestine
15	chr11:102277200-102284200	Weak transcription	Aorta	Aorta
16	chr11:102277200-102284200	Weak transcription	Lung	lung
17	chr11:102277200-102284200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:102277200-102285600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:102277200-102297000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr11:102277400-102283200	Weak transcription	Adipose Nuclei	Adipose
21	chr11:102278000-102284200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:102278200-102289600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:102278600-102287200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:102278600-102300600	Weak transcription	Esophagus	oesophagus
25	chr11:102278800-102282400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:102279000-102281800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:102279200-102281800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr11:102279400-102282200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:102279400-102285200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:102279600-102282400	Strong transcription	HepG2	liver
31	chr11:102279600-102282600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:102280200-102282800	Strong transcription	Liver	Liver
33	chr11:102280200-102284400	Strong transcription	Fetal Intestine Small	intestine
34	chr11:102280400-102281800	Strong transcription	Thymus	Thymus
35	chr11:102280400-102282200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:102280400-102282400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr11:102280400-102282800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr11:102280600-102282800	Strong transcription	GM12878-XiMat	blood
39	chr11:102280800-102281800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:102280800-102281800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr11:102280800-102281800	Enhancers	Osteobl	bone
42	chr11:102280800-102282000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:102280800-102282400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:102280800-102282400	Genic enhancers	Primary T cells from cord blood	blood
45	chr11:102280800-102282400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:102280800-102283200	Enhancers	NHDF-Ad	bronchial
47	chr11:102280800-102284000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr11:102280800-102285400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr11:102281000-102282200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:102281000-102282200	Enhancers	K562	blood

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