Variant report

Variant	rs4150550
Chromosome Location	chr11:18350898-18350899
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr11:18350468-18351091	K562	blood:	n/a	chr11:18350604-18350612
2	ZC3H11A	chr11:18350783-18351205	K562	blood:	n/a	n/a
3	RFX5	chr11:18350643-18351130	Hela-S3	cervix:	n/a	n/a
4	NFE2	chr11:18350650-18351010	K562	blood:	n/a	chr11:18350824-18350839
5	STAT3	chr11:18350687-18351006	MCF10A-Er-Src	breast:	n/a	n/a
6	IRF1	chr11:18350433-18351043	K562	blood:	n/a	n/a
7	PAX5	chr11:18350655-18351291	GM12878	blood:	n/a	chr11:18350961-18350979 chr11:18350970-18350979
8	BACH1	chr11:18350671-18350985	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA1	chr11:18350500-18351747	PBDE	blood:	n/a	chr11:18350670-18350680 chr11:18350661-18350678 chr11:18350670-18350679 chr11:18350672-18350679 chr11:18350668-18350681
10	YY1	chr11:18350816-18351304	GM12891	blood:	n/a	chr11:18351163-18351173
11	YY1	chr11:18350759-18351061	K562	blood:	n/a	n/a
12	TAL1	chr11:18350604-18351023	K562	blood:	n/a	chr11:18350661-18350679
13	PBX3	chr11:18350410-18351156	SK-N-SH	brain:	n/a	n/a
14	MAX	chr11:18350721-18351120	K562	blood:	n/a	n/a
15	EP300	chr11:18350607-18351154	K562	blood:	n/a	n/a
16	BACH1	chr11:18350562-18351200	K562	blood:	n/a	n/a
17	TBL1XR1	chr11:18350489-18351021	K562	blood:	n/a	n/a
18	USF2	chr11:18350743-18351023	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr11:18350790-18351157	MCF10A-Er-Src	breast:	n/a	n/a
20	CCNT2	chr11:18350726-18351099	K562	blood:	n/a	n/a
21	EP300	chr11:18350588-18351016	Hela-S3	cervix:	n/a	n/a
22	FOXM1	chr11:18350412-18351059	MCF-7	breast:	n/a	n/a
23	JUND	chr11:18350632-18351113	K562	blood:	n/a	n/a
24	FOSL2	chr11:18350610-18351051	MCF-7	breast:	n/a	n/a
25	PAX5	chr11:18350798-18351089	GM12878	blood:	n/a	chr11:18350961-18350979 chr11:18350970-18350979
26	POLR2A	chr11:18350812-18351051	GM12891	blood:	n/a	n/a
27	ARID3A	chr11:18350394-18351028	K562	blood:	n/a	chr11:18350742-18350758 chr11:18350741-18350757
28	NFIC	chr11:18350670-18351504	GM12878	blood:	n/a	n/a
29	GATA3	chr11:18350585-18351144	SK-N-SH	brain:	n/a	chr11:18350670-18350680 chr11:18350661-18350678 chr11:18350670-18350679 chr11:18350672-18350679 chr11:18350668-18350681 chr11:18350868-18350876
30	PAX5	chr11:18350871-18351140	GM12891	blood:	n/a	chr11:18350961-18350979 chr11:18350970-18350979
31	STAT3	chr11:18350804-18351290	GM12878	blood:	n/a	n/a
32	MAX	chr11:18350741-18351075	Hela-S3	cervix:	n/a	n/a
33	GATA3	chr11:18350445-18351181	MCF-7	breast:	n/a	chr11:18350670-18350680 chr11:18350661-18350678 chr11:18350670-18350679 chr11:18350672-18350679 chr11:18350668-18350681 chr11:18350868-18350876
34	POLR2A	chr11:18350881-18351278	GM12892	blood:	n/a	n/a
35	MYC	chr11:18350516-18351119	K562	blood:	n/a	n/a
36	IKZF1	chr11:18350771-18351425	GM12878	blood:	n/a	n/a
37	FOS	chr11:18350642-18351002	MCF10A-Er-Src	breast:	n/a	n/a
38	ATF3	chr11:18350717-18350986	K562	blood:	n/a	n/a
39	TCF12	chr11:18350449-18351219	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr11:18350310-18351991	K562	blood:	n/a	n/a
41	RAD21	chr11:18350706-18351003	Hela-S3	cervix:	n/a	n/a
42	JUN	chr11:18350479-18352119	K562	blood:	n/a	chr11:18350604-18350612
43	PAX5	chr11:18350745-18351350	GM12878	blood:	n/a	chr11:18350961-18350979 chr11:18350970-18350979
44	FOSL1	chr11:18350755-18350998	K562	blood:	n/a	n/a
45	FOS	chr11:18350641-18351239	MCF10A-Er-Src	breast:	n/a	n/a
46	MAFF	chr11:18350616-18351270	K562	blood:	n/a	chr11:18350823-18350841
47	POLR2A	chr11:18350680-18351561	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr11:18350588-18351022	SK-N-SH	brain:	n/a	n/a
49	MAZ	chr11:18350703-18351189	K562	blood:	n/a	n/a
50	YY1	chr11:18350809-18351152	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:18342879..18346241-chr11:18346771..18352447,12	MCF-7	breast:
2	chr11:18349490..18352307-chr11:18416120..18418950,3	MCF-7	breast:
3	chr11:18350549..18352457-chr11:18378892..18380710,2	K562	blood:
4	chr11:18350526..18353527-chr11:18357555..18360928,3	K562	blood:
5	chr11:18350460..18352865-chr11:18416240..18418848,2	K562	blood:
6	chr11:18349981..18351945-chr11:18404895..18407239,2	MCF-7	breast:
7	chr11:18349169..18352444-chr11:18352631..18354865,4	K562	blood:
8	chr11:18350612..18353421-chr11:18414692..18417585,3	MCF-7	breast:
9	chr11:18350532..18352791-chr11:18365222..18367749,2	K562	blood:

Variant related genes	Relation type
GTF2H1	TF binding region
ENSG00000110756	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10734259	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741742	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832917	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10832921	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024634	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1140047	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12293544	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124374	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3740711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3802968	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150526	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150566	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150588	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150609	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4150650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150653	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757637	1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7103375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7129995	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7947378	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9783347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9988866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.94[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	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	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
3	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
rs4150550	GTF2H1	cis	Stomach	GTEx
rs4150550	GTF2H1	cis	Esophagus Muscularis	GTEx
rs4150550	GTF2H1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18344800-18353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:18345000-18353400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:18346200-18351400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:18346200-18351400	Weak transcription	Right Atrium	heart
7	chr11:18346200-18352000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:18346200-18352600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:18346200-18355200	Weak transcription	Colonic Mucosa	Colon
10	chr11:18346400-18353000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:18346400-18353400	Weak transcription	Pancreas	Pancrea
12	chr11:18346400-18354600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:18346400-18355200	Weak transcription	Gastric	stomach
14	chr11:18346400-18355200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:18346400-18357000	Weak transcription	Esophagus	oesophagus
16	chr11:18346400-18358400	Weak transcription	Right Ventricle	heart
17	chr11:18346400-18358600	Weak transcription	Fetal Brain Male	brain
18	chr11:18346600-18351400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:18346600-18352200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:18346600-18353200	Weak transcription	Brain Germinal Matrix	brain
21	chr11:18346600-18355200	Weak transcription	Fetal Kidney	kidney
22	chr11:18346600-18355200	Weak transcription	Ovary	ovary
23	chr11:18346800-18351200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:18346800-18352000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:18346800-18352400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:18346800-18353200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:18346800-18354400	Weak transcription	NHLF	lung
28	chr11:18346800-18354600	Weak transcription	Brain Angular Gyrus	brain
29	chr11:18346800-18354600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:18346800-18354600	Weak transcription	HSMMtube	muscle
31	chr11:18346800-18355000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:18346800-18355000	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:18346800-18355000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:18346800-18355200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:18346800-18372000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:18347000-18351800	Weak transcription	Brain Anterior Caudate	brain
39	chr11:18347000-18351800	Weak transcription	Brain Substantia Nigra	brain
40	chr11:18347000-18353000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:18347000-18372400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr11:18347200-18351000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:18347200-18351800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:18347400-18366800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr11:18347400-18371200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr11:18347800-18351000	Strong transcription	Fetal Intestine Small	intestine
48	chr11:18347800-18351000	Strong transcription	Fetal Stomach	stomach
49	chr11:18347800-18351400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:18347800-18353600	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links