Variant report

Variant	rs1002227
Chromosome Location	chr11:17405347-17405348
allele	G/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17405197..17406140-chr11:17492660..17493631,2	K562	blood:
2	chr11:17405241..17406227-chr11:17551569..17552408,2	MCF-7	breast:
3	chr11:17405241..17406080-chr11:17492901..17493668,2	MCF-7	breast:
4	chr11:17405241..17405887-chr11:17492811..17493698,3	MCF-7	breast:
5	chr11:17405141..17406113-chr11:17549390..17550226,4	K562	blood:
6	chr11:17404945..17405792-chr11:17525735..17526346,2	MCF-7	breast:
7	chr11:17405274..17406188-chr11:17494608..17495575,4	MCF-7	breast:
8	chr11:17251318..17252261-chr11:17405052..17406043,5	MCF-7	breast:
9	chr11:17373252..17376530-chr11:17405235..17408726,4	K562	blood:
10	chr11:17399571..17401205-chr11:17403779..17406500,2	K562	blood:
11	chr11:17403459..17406167-chr11:17526057..17528257,2	K562	blood:
12	chr11:17404201..17406453-chr11:17548482..17550709,2	K562	blood:
13	chr11:17405170..17406511-chr11:17549006..17550272,4	MCF-7	breast:
14	chr11:17405126..17405972-chr11:17525824..17526796,7	MCF-7	breast:
15	chr11:17405333..17406124-chr11:17519578..17520279,2	MCF-7	breast:
16	chr11:17405209..17406183-chr11:17527113..17528432,4	MCF-7	breast:
17	chr11:17405017..17406217-chr11:17525833..17526983,7	K562	blood:
18	chr11:17375991..17376649-chr11:17405080..17405838,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188211	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10466382	1.00[ASW][hapmap];0.89[CEU][hapmap]
rs10734253	0.93[ASN][1000 genomes]
rs10766383	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10766384	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10766385	0.82[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10766389	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs10766391	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10766392	0.81[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766395	0.95[ASN][1000 genomes]
rs10766396	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832757	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10832765	0.82[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10832768	0.82[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10832769	0.89[CEU][hapmap]
rs10832770	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs10832779	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10832784	0.97[ASN][1000 genomes]
rs10832785	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11024251	0.89[CEU][hapmap]
rs11024273	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024275	0.83[EUR][1000 genomes]
rs1557764	0.97[ASN][1000 genomes]
rs2067043	0.80[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2074312	0.80[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2074313	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2079042	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2214295	0.95[ASN][1000 genomes]
rs2285676	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34327804	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35762444	0.91[ASN][1000 genomes]
rs3741203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282912	0.88[EUR][1000 genomes]
rs4148638	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs5210	0.93[ASN][1000 genomes]
rs5218	1.00[ASW][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5222	0.91[ASN][1000 genomes]
rs7112030	0.87[ASN][1000 genomes]
rs7112138	0.87[ASN][1000 genomes]
rs71484767	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs886288	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9633836	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645621	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv467712	chr11:17393644-17418477	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv553583	chr11:17393644-17418477	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv517772	chr11:17401134-17427862	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv897018	chr11:17403639-17417337	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv528959	chr11:17403639-17435214	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv540951	chr11:17404438-17422755	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1002227	GTF2H1	cis	cerebellum	SCAN
rs1002227	LOC494141	cis	lymphoblastoid	seeQTL
rs1002227	DKFZp686O24166	cis	cerebellum	SCAN
rs1002227	ABCC8	cis	parietal	SCAN
rs1002227	KCNJ11	cis	Esophagus Mucosa	GTEx
rs1002227	NUCB2	cis	cerebellum	SCAN
rs1002227	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs1002227	GTF2H1	cis	parietal	SCAN
rs1002227	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs1002227	TSG101	cis	cerebellum	SCAN
rs1002227	PTH	cis	cerebellum	SCAN
rs1002227	ABCC8	cis	cerebellum	SCAN
rs1002227	KCNJ11	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17394200-17407600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:17394400-17410200	Weak transcription	A549	lung
3	chr11:17395200-17405800	Weak transcription	Gastric	stomach
4	chr11:17395200-17410200	Weak transcription	Thymus	Thymus
5	chr11:17395600-17406200	Weak transcription	Pancreas	Pancrea
6	chr11:17395600-17410200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:17395600-17410400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:17395800-17405400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:17395800-17405400	Weak transcription	Left Ventricle	heart
10	chr11:17395800-17409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:17396000-17408800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:17396600-17410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:17397200-17407800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:17398200-17410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:17398400-17405400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:17398800-17410200	Weak transcription	Primary T cells from cord blood	blood
17	chr11:17400600-17408000	Strong transcription	Fetal Intestine Small	intestine
18	chr11:17400600-17408800	Weak transcription	Brain Germinal Matrix	brain
19	chr11:17400800-17407200	Weak transcription	Fetal Brain Female	brain
20	chr11:17400800-17410200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:17401000-17405600	Weak transcription	Brain Hippocampus Middle	brain
22	chr11:17401000-17410200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:17401200-17405400	Weak transcription	Psoas Muscle	Psoas
24	chr11:17401200-17407200	Weak transcription	Lung	lung
25	chr11:17401600-17410200	Weak transcription	Hela-S3	cervix
26	chr11:17401600-17410200	Weak transcription	K562	blood
27	chr11:17401800-17405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:17401800-17405600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:17401800-17407400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:17401800-17407400	Weak transcription	HepG2	liver
31	chr11:17401800-17410200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:17402000-17410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:17402000-17410200	Weak transcription	HMEC	breast
34	chr11:17402400-17407800	Weak transcription	Fetal Intestine Large	intestine
35	chr11:17403000-17405400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:17403000-17410400	Weak transcription	Aorta	Aorta
37	chr11:17403200-17406200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr11:17403600-17408600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr11:17403800-17410400	Weak transcription	HSMMtube	muscle
40	chr11:17404000-17408000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:17404200-17405600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:17404200-17405600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:17404200-17405800	Weak transcription	Right Ventricle	heart
44	chr11:17404200-17406000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:17404200-17410200	Weak transcription	HSMM	muscle
46	chr11:17404400-17405600	Enhancers	Fetal Heart	heart
47	chr11:17404400-17407600	Weak transcription	Right Atrium	heart
48	chr11:17404600-17405400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr11:17404600-17405600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr11:17404800-17405400	Strong transcription	Fetal Muscle Leg	muscle

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