Variant report

Variant	rs11770186
Chromosome Location	chr7:25894232-25894233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:25614579..25616228-chr7:25892925..25895334,2	K562	blood:
2	chr7:25889535..25891445-chr7:25893362..25896566,3	MCF-7	breast:
3	chr7:25893918..25894862-chr7:25932230..25933199,2	K562	blood:
4	chr7:25163296..25164829-chr7:25893486..25896365,2	MCF-7	breast:
5	chr7:25893947..25899810-chr7:26238759..26243593,6	K562	blood:
6	chr7:25893945..25894718-chr7:26404689..26405336,3	MCF-7	breast:
7	chr7:25893800..25898221-chr7:26239034..26243289,6	MCF-7	breast:
8	chr7:25805754..25807297-chr7:25892991..25895068,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10225976	0.89[ASN][1000 genomes]
rs10238703	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10241634	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241659	0.85[ASN][1000 genomes]
rs10242536	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10245353	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10260677	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10262483	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10267498	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10271088	0.85[ASN][1000 genomes]
rs10271460	0.85[ASN][1000 genomes]
rs10274306	0.85[ASN][1000 genomes]
rs10282436	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1055144	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951112	0.89[EUR][1000 genomes]
rs12666961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451382	0.83[ASN][1000 genomes]
rs1451385	0.83[CEU][hapmap]
rs2391168	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28392961	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28473292	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28858973	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893220	0.85[ASN][1000 genomes]
rs2893221	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35766302	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4141278	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41469349	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4722530	0.92[EUR][1000 genomes]
rs56376645	0.91[ASN][1000 genomes]
rs57246313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60643312	0.87[ASN][1000 genomes]
rs61140461	0.85[ASN][1000 genomes]
rs62447896	0.83[ASN][1000 genomes]
rs73093663	0.81[AFR][1000 genomes]
rs7782246	0.85[ASN][1000 genomes]
rs7782292	0.85[ASN][1000 genomes]
rs7798002	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7798130	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7798431	0.83[ASN][1000 genomes]
rs966042	0.84[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9987000	0.92[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	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830928	chr7:25820147-25965014	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11770186	SKAP2	cis	cerebellum	SCAN
rs11770186	CCDC126	cis	parietal	SCAN
rs11770186	TRIL	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25890200-25895200	Weak transcription	HSMMtube	muscle
2	chr7:25891800-25894400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:25892400-25894400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:25892400-25894400	Bivalent Enhancer	Fetal Stomach	stomach
5	chr7:25892600-25894600	Bivalent Enhancer	Fetal Lung	lung
6	chr7:25892800-25896200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:25893000-25894800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:25893000-25894800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:25893000-25894800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr7:25893000-25895000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:25893200-25894400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr7:25893400-25894400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:25893400-25894600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
14	chr7:25893400-25894600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:25893400-25896400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:25893400-25898000	Active TSS	NHDF-Ad	bronchial
17	chr7:25893600-25894600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr7:25893600-25894600	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr7:25893600-25894600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr7:25893600-25894600	Flanking Active TSS	Osteobl	bone
21	chr7:25893800-25894400	Bivalent Enhancer	Adipose Nuclei	Adipose
22	chr7:25893800-25894400	Enhancers	HUVEC	blood vessel
23	chr7:25893800-25894600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr7:25893800-25894600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr7:25893800-25894600	Enhancers	HSMM	muscle
26	chr7:25894000-25894400	Weak transcription	Psoas Muscle	Psoas
27	chr7:25894000-25894400	Bivalent/Poised TSS	A549	lung
28	chr7:25894000-25894600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr7:25894000-25894600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr7:25894000-25894600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:25894000-25894600	Bivalent Enhancer	Colon Smooth Muscle	Colon
32	chr7:25894000-25894600	Enhancers	Rectal Smooth Muscle	rectum
33	chr7:25894000-25894800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
34	chr7:25894000-25895000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
35	chr7:25894000-25895000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr7:25894000-25896000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:25894000-25896800	Active TSS	Stomach Smooth Muscle	stomach
38	chr7:25894000-25897000	Active TSS	K562	blood
39	chr7:25894000-25897200	Active TSS	Aorta	Aorta
40	chr7:25894000-25897400	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr7:25894000-25897800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:25894200-25894400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr7:25894200-25894400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
44	chr7:25894200-25894400	Bivalent Enhancer	Fetal Intestine Large	intestine
45	chr7:25894200-25894400	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
46	chr7:25894200-25894400	Enhancers	NHEK	skin
47	chr7:25894200-25894400	Active TSS	NHLF	lung
48	chr7:25894200-25894600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:25894200-25894600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr7:25894200-25894800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

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