Variant report

Variant	rs10741742
Chromosome Location	chr11:18342160-18342161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:18342054-18344907	Hela-S3	cervix:	n/a	n/a
2	UBTF	chr11:18342088-18342365	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18270589..18272297-chr11:18340859..18342793,2	K562	blood:
2	chr11:18339772..18342486-chr11:18375558..18377297,2	K562	blood:
3	chr11:18340850..18343289-chr11:18360894..18362433,2	K562	blood:
4	chr11:18340646..18350403-chr11:18414573..18418572,22	K562	blood:
5	chr11:18341846..18344494-chr11:18547115..18549354,2	MCF-7	breast:
6	chr11:18336552..18338085-chr11:18340348..18343052,2	MCF-7	breast:
7	chr11:18328369..18330442-chr11:18341510..18343181,2	K562	blood:
8	chr11:18307340..18310591-chr11:18340181..18344104,5	MCF-7	breast:
9	chr11:18340586..18347042-chr11:18413380..18419628,16	K562	blood:

No data

Variant related genes	Relation type
GTF2H1	TF binding region
ENSG00000074319	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000110756	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10734259	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741741	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832917	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10832921	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024634	0.91[EUR][1000 genomes]
rs1140047	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12286683	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12293544	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1520884	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061164	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124374	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3740711	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3802968	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3825025	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150526	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150550	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150561	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150564	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150566	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150575	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150588	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150610	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150612	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150622	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150641	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150642	0.88[ASN][1000 genomes]
rs4150650	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150651	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150653	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150655	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150661	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150673	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4353250	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486419	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7129995	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7947378	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9783347	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9988866	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10741742	GTF2H1	cis	Esophagus Mucosa	GTEx
rs10741742	GTF2H1	cis	Stomach	GTEx
rs10741742	GTF2H1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18311800-18343000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18317200-18342200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:18327800-18342200	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:18327800-18342200	Weak transcription	HUVEC	blood vessel
5	chr11:18331000-18342200	Weak transcription	Right Ventricle	heart
6	chr11:18332200-18342200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:18332600-18342800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:18332600-18342800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:18332600-18343000	Weak transcription	Lung	lung
10	chr11:18332800-18342200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:18332800-18342200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:18332800-18342800	Weak transcription	Fetal Brain Male	brain
13	chr11:18333000-18342200	Weak transcription	Adipose Nuclei	Adipose
14	chr11:18333000-18342400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:18333000-18342400	Weak transcription	Colonic Mucosa	Colon
16	chr11:18333000-18342800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:18333000-18342800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:18333200-18342200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:18334400-18342800	Weak transcription	Fetal Thymus	thymus
20	chr11:18334400-18343000	Weak transcription	Esophagus	oesophagus
21	chr11:18334400-18343200	Weak transcription	Pancreas	Pancrea
22	chr11:18334600-18342200	Weak transcription	Brain Angular Gyrus	brain
23	chr11:18334600-18342200	Weak transcription	Brain Anterior Caudate	brain
24	chr11:18334600-18342200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:18334600-18342200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:18335800-18342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:18335800-18342800	Weak transcription	Ovary	ovary
28	chr11:18336400-18342800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:18336600-18342800	Weak transcription	Fetal Muscle Leg	muscle
30	chr11:18337000-18343000	Weak transcription	Left Ventricle	heart
31	chr11:18337000-18343400	Weak transcription	Spleen	Spleen
32	chr11:18337800-18342200	Weak transcription	Fetal Brain Female	brain
33	chr11:18337800-18343000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:18337800-18343400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:18338200-18342200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:18338200-18342800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:18338400-18342200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:18338600-18342800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:18339800-18342200	Weak transcription	Stomach Mucosa	stomach
40	chr11:18340000-18342200	Weak transcription	Fetal Heart	heart
41	chr11:18340000-18342800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:18340000-18345200	Active TSS	GM12878-XiMat	blood
43	chr11:18340800-18342200	Enhancers	Primary T cells from cord blood	blood
44	chr11:18340800-18342200	Enhancers	Small Intestine	intestine
45	chr11:18340800-18342800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr11:18341000-18342800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr11:18341000-18342800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr11:18341000-18342800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr11:18341000-18346000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:18341200-18342200	Enhancers	Brain Hippocampus Middle	brain

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