Variant report

Variant	rs10741743
Chromosome Location	chr11:18347994-18347995
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18342879..18346241-chr11:18346771..18352447,12	MCF-7	breast:
2	chr11:18340646..18350403-chr11:18414573..18418572,22	K562	blood:
3	chr11:18347485..18350857-chr11:18414305..18419253,5	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000110768	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10741740	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10766467	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10766469	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10766471	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10832919	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832920	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832923	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024606	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024613	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024622	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12294486	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2037867	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305564	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2403254	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150581	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150589	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150606	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150628	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150644	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4150678	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4596	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60889939	0.86[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10741743	GTF2H1	cis	lung	GTEx
rs10741743	GTF2H1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18344800-18349000	Weak transcription	Lung	lung
2	chr11:18344800-18353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:18345000-18353400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:18345200-18350800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:18345600-18350800	Weak transcription	Aorta	Aorta
8	chr11:18345800-18349400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:18346000-18349600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:18346200-18348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:18346200-18348600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:18346200-18349200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:18346200-18349400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:18346200-18351400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:18346200-18351400	Weak transcription	Right Atrium	heart
16	chr11:18346200-18352000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:18346200-18352600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:18346200-18355200	Weak transcription	Colonic Mucosa	Colon
19	chr11:18346400-18349000	Weak transcription	Thymus	Thymus
20	chr11:18346400-18349000	Weak transcription	Spleen	Spleen
21	chr11:18346400-18349400	Strong transcription	Psoas Muscle	Psoas
22	chr11:18346400-18350000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:18346400-18353000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:18346400-18353400	Weak transcription	Pancreas	Pancrea
25	chr11:18346400-18354600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:18346400-18355200	Weak transcription	Gastric	stomach
27	chr11:18346400-18355200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:18346400-18357000	Weak transcription	Esophagus	oesophagus
29	chr11:18346400-18358400	Weak transcription	Right Ventricle	heart
30	chr11:18346400-18358600	Weak transcription	Fetal Brain Male	brain
31	chr11:18346600-18348000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr11:18346600-18348000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:18346600-18348200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:18346600-18349000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:18346600-18349200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr11:18346600-18349400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:18346600-18349400	Strong transcription	Placenta	Placenta
38	chr11:18346600-18349600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:18346600-18349800	Strong transcription	Fetal Thymus	thymus
40	chr11:18346600-18350400	Weak transcription	Stomach Mucosa	stomach
41	chr11:18346600-18350600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:18346600-18350600	Weak transcription	NH-A	brain
43	chr11:18346600-18350800	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:18346600-18351400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:18346600-18352200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:18346600-18353200	Weak transcription	Brain Germinal Matrix	brain
47	chr11:18346600-18355200	Weak transcription	Fetal Kidney	kidney
48	chr11:18346600-18355200	Weak transcription	Ovary	ovary
49	chr11:18346800-18348000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr11:18346800-18348200	Genic enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links