Variant report

Variant	rs11729106
Chromosome Location	chr4:76420045-76420046
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	CEBPB	chr4:76419794-76420104	A549	lung:	n/a	n/a
2	FOS	chr4:76419761-76420131	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr4:76419761-76420113	K562	blood:	n/a	n/a
4	CEBPB	chr4:76419765-76420145	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr4:76419963-76420104	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr4:76419762-76420103	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr4:76419758-76420163	MCF10A-Er-Src	breast:	n/a	chr4:76419916-76419927
8	MAFK	chr4:76419831-76420094	IMR90	lung:	n/a	n/a
9	FOS	chr4:76419699-76420171	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr4:76419793-76420219	A549	lung:	n/a	n/a
11	FOS	chr4:76419778-76420105	MCF10A-Er-Src	breast:	n/a	n/a
12	RCOR1	chr4:76419401-76420278	IMR90	lung:	n/a	n/a
13	POLR2A	chr4:76420034-76420082	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr4:76419758-76420112	MCF10A-Er-Src	breast:	n/a	chr4:76419916-76419927
15	CEBPB	chr4:76419804-76420108	MCF-7	breast:	n/a	n/a
16	FOS	chr4:76419755-76420163	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr4:76419707-76420111	MCF10A-Er-Src	breast:	n/a	chr4:76419916-76419927
18	CEBPB	chr4:76419737-76420081	MCF-7	breast:	n/a	n/a
19	MYC	chr4:76419761-76420163	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr4:76419754-76420152	IMR90	lung:	n/a	n/a
21	E2F4	chr4:76419818-76420088	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr4:76419731-76420143	MCF10A-Er-Src	breast:	n/a	chr4:76419916-76419927

Variant related genes	Relation type
RCHY1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10009558	0.83[YRI][hapmap]
rs10518140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721925	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11722278	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11727806	0.97[EUR][1000 genomes]
rs11732511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644911	0.82[ASN][1000 genomes]
rs12648028	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12648354	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1351094	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1904104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2126854	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2306177	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867919	0.83[ASN][1000 genomes]
rs2903701	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57275697	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6836107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845472	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6845588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847297	0.84[ASN][1000 genomes]
rs6851699	0.84[ASN][1000 genomes]
rs7673610	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7683530	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs9307834	0.81[YRI][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11729106	THAP6	cis	multi-tissue	Pritchard
rs11729106	RCHY1	Cis_1M	lymphoblastoid	RTeQTL
rs11729106	THAP6	cis	Lymphoblastoid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
3	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
4	chr4:76395800-76437000	Weak transcription	Lung	lung
5	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
6	chr4:76396200-76424400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
8	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
13	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
14	chr4:76402200-76422000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:76402200-76423000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:76402200-76425800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr4:76402400-76425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:76402600-76423200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:76403000-76423800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:76403800-76433600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:76404400-76422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:76404800-76422800	Strong transcription	Dnd41	blood
23	chr4:76405400-76422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:76405600-76434400	Weak transcription	Fetal Heart	heart
25	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:76407800-76424600	Weak transcription	Fetal Brain Male	brain
28	chr4:76408000-76424600	Weak transcription	Ovary	ovary
29	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
30	chr4:76409400-76425800	Strong transcription	Fetal Thymus	thymus
31	chr4:76409600-76423800	Weak transcription	Fetal Brain Female	brain
32	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:76410400-76421000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:76410400-76425600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr4:76411400-76435400	Weak transcription	Small Intestine	intestine
36	chr4:76412200-76425000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:76413200-76422000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:76413200-76422000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:76413400-76422000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr4:76413400-76423000	Strong transcription	Primary B cells from cord blood	blood
41	chr4:76414600-76427000	Weak transcription	Fetal Stomach	stomach
42	chr4:76414600-76429400	Weak transcription	HSMMtube	muscle
43	chr4:76415000-76424600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:76415200-76420600	Weak transcription	K562	blood
45	chr4:76415200-76423400	Weak transcription	Psoas Muscle	Psoas
46	chr4:76415200-76428200	Weak transcription	A549	lung
47	chr4:76415400-76421200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:76415400-76421400	Weak transcription	Thymus	Thymus
49	chr4:76415400-76424000	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:76415400-76430200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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