Variant report

Variant	rs10770129
Chromosome Location	chr11:10674671-10674672
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:10674645-10674695	SAEC	small airway:	n/a
2	chr11:10674645-10674695	GM06990	blood:	n/a
3	chr11:10674645-10674695	PrEC	prostate:	n/a
4	chr11:10674645-10674695	Hepatocyte	liver:	n/a
5	chr11:10674645-10674695	Jurkat	blood:	n/a
6	chr11:10674645-10674695	PANC-1	pancreas:	n/a
7	chr11:10674645-10674695	HL-60	blood:	n/a
8	chr11:10674645-10674695	SK-N-SH_RA	brain:	n/a
9	chr11:10674645-10674695	HCF	heart:	n/a
10	chr11:10674645-10674695	AG10803	skin:	n/a
11	chr11:10674645-10674695	MCF10A-Er-Src	breast:	n/a
12	chr11:10674645-10674695	ovcar-3	ovarian:	n/a
13	chr11:10674645-10674695	MCF-7	breast:	n/a
14	chr11:10674645-10674695	H1-hESC	embryonic stem cell:	embryo
15	chr11:10674645-10674695	K562	blood:	n/a
16	chr11:10674645-10674695	HepG2	liver:	n/a
17	chr11:10674645-10674695	SKMC	muscle:	n/a
18	chr11:10674645-10674695	HRPEpiC	eye:	n/a
19	chr11:10674645-10674695	GM19239	blood:	n/a
20	chr11:10674645-10674695	GM12878	blood:	n/a
21	chr11:10674645-10674695	HRCEpiC	kidney:	n/a
22	chr11:10674645-10674695	HMEC	breast:	n/a
23	chr11:10674645-10674695	HAEpiC	amniotic membrane:	n/a
24	chr11:10674645-10674695	RPTEC	kidney:	n/a
25	chr11:10674645-10674695	HEEpiC	esophagus:	n/a
26	chr11:10674645-10674695	AG09319	gingival:	n/a
27	chr11:10674645-10674695	NHDF-neo	bronchial:	n/a
28	chr11:10674645-10674695	SK-N-SH	brain:	n/a
29	chr11:10674645-10674695	HNPCEpiC	eye:	n/a
30	chr11:10674645-10674695	AG04450	lung:	fetal
31	chr11:10674645-10674695	A549	lung:	n/a
32	chr11:10674645-10674695	LNCaP	prostate:	n/a
33	chr11:10674645-10674695	HRE	kidney:	n/a
34	chr11:10674645-10674695	NHBE	bronchial:	n/a
35	chr11:10674645-10674695	ECC-1	luminal epithelium:	n/a
36	chr11:10674645-10674695	SK-N-MC	brain:	n/a
37	chr11:10674645-10674695	HCM	heart:	n/a
38	chr11:10674645-10674695	GM12891	blood:	n/a
39	chr11:10674645-10674695	BE2_C	brain:	n/a
40	chr11:10674645-10674695	IMR90	lung:	fetal
41	chr11:10674645-10674695	HCT-116	colon:	n/a
42	chr11:10674645-10674695	HCPEpiC	choroid plexus:	n/a
43	chr11:10674645-10674695	PFSK-1	brain:	n/a
44	chr11:10674645-10674695	HIPEpiC	eye:	n/a
45	chr11:10674645-10674695	Caco-2	colon:	n/a
46	chr11:10674645-10674695	T-47D	breast:	n/a
47	chr11:10674645-10674695	CMK	blood:	n/a
48	chr11:10674645-10674695	HEK293	kidney:	embryo
49	chr11:10674645-10674695	AoSMC	blood vessel:	n/a
50	chr11:10674645-10674695	AG09309	skin:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:10584920..10587068-chr11:10674559..10677361,2	K562	blood:
2	chr11:10322610..10325546-chr11:10673380..10676333,2	K562	blood:
3	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:

No data

Variant related genes	Relation type
MRVI1	CpG island
ENSG00000110315	Chromatin interaction
ENSG00000254554	Chromatin interaction
ENSG00000177112	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10431031	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10770128	1.00[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10770130	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10770132	0.84[JPT][hapmap]
rs10770133	0.84[JPT][hapmap]
rs10840451	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840454	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840455	0.95[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840458	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10840460	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840461	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840462	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840463	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840464	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840465	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840466	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840467	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10840468	0.84[JPT][hapmap]
rs11042909	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042910	0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11042911	0.84[JPT][hapmap]
rs11042913	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12295574	0.86[ASN][1000 genomes]
rs1390572	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1425149	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1425150	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1425151	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1544862	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1544863	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1559652	0.81[ASN][1000 genomes]
rs16908157	0.84[JPT][hapmap]
rs16908159	0.84[JPT][hapmap]
rs16908162	0.84[JPT][hapmap]
rs1845832	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1874444	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1895712	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2033049	0.90[ASN][1000 genomes]
rs2098840	0.84[ASN][1000 genomes]
rs35040034	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3993279	0.89[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4909943	0.89[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4909944	0.93[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4910166	0.82[JPT][hapmap]
rs7113409	0.80[ASN][1000 genomes]
rs7123106	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7127014	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs722274	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7933525	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7935285	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7938635	0.95[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7939662	0.83[JPT][hapmap]
rs7939686	0.84[JPT][hapmap]
rs9633862	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9633863	0.91[AMR][1000 genomes];0.91[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10770129	GVIN1	cis	cerebellum	SCAN
rs10770129	PLA2G7	trans	parietal	SCAN
rs10770129	RRAS2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
4	chr11:10658800-10676600	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:10664400-10675000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:10669600-10675600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:10669600-10676800	Weak transcription	Fetal Intestine Large	intestine
9	chr11:10670200-10675000	Weak transcription	K562	blood
10	chr11:10670400-10675400	Genic enhancers	Fetal Stomach	stomach
11	chr11:10670800-10675000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:10670800-10676400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:10671000-10676200	Weak transcription	A549	lung
14	chr11:10671400-10676000	Enhancers	Brain Anterior Caudate	brain
15	chr11:10671400-10676200	Enhancers	Brain Hippocampus Middle	brain
16	chr11:10671400-10677000	Weak transcription	Fetal Intestine Small	intestine
17	chr11:10672000-10679200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr11:10672400-10675000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:10672600-10674800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:10673000-10682200	Enhancers	Placenta	Placenta
21	chr11:10673200-10675800	Enhancers	Lung	lung
22	chr11:10673200-10676200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:10673200-10676800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:10673200-10677800	Enhancers	Colon Smooth Muscle	Colon
25	chr11:10673400-10674800	Enhancers	Colonic Mucosa	Colon
26	chr11:10673400-10675200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr11:10673400-10676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:10673400-10676600	Enhancers	Spleen	Spleen
29	chr11:10673400-10679200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr11:10673400-10682800	Enhancers	Ovary	ovary
31	chr11:10673600-10675200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:10673600-10675400	Weak transcription	GM12878-XiMat	blood
33	chr11:10673600-10678400	Weak transcription	Left Ventricle	heart
34	chr11:10673600-10678400	Weak transcription	Right Atrium	heart
35	chr11:10673800-10675400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:10673800-10676200	Weak transcription	Osteobl	bone
37	chr11:10673800-10678800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:10673800-10679200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr11:10673800-10681400	Weak transcription	Pancreas	Pancrea
40	chr11:10674000-10675800	Enhancers	Esophagus	oesophagus
41	chr11:10674000-10676000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:10674000-10676200	Enhancers	Brain Substantia Nigra	brain
43	chr11:10674000-10676400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:10674000-10676600	Weak transcription	NH-A	brain
45	chr11:10674000-10677200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:10674000-10677400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:10674000-10681400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:10674200-10676600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr11:10674200-10681800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr11:10674400-10674800	Flanking Active TSS	Rectal Smooth Muscle	rectum

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