Variant report

Variant	rs9356477
Chromosome Location	chr6:166738902-166738903
allele	A/T
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	TCF12	chr6:166738872-166739117	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:166736292-166741360	K562	blood:	n/a	n/a
3	EP300	chr6:166738833-166739642	GM12878	blood:	n/a	chr6:166739110-166739126 chr6:166739006-166739020
4	RUNX3	chr6:166738765-166739261	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:166738823-166739474	GM12878	blood:	n/a	n/a
6	SIN3A	chr6:166738899-166739428	GM12878	blood:	n/a	n/a
7	RFX5	chr6:166738893-166739342	GM12878	blood:	n/a	n/a
8	EP300	chr6:166738814-166739624	GM12878	blood:	n/a	chr6:166739110-166739126 chr6:166739006-166739020
9	NFATC1	chr6:166738782-166739492	GM12878	blood:	n/a	n/a
10	CHD1	chr6:166738850-166739404	GM12878	blood:	n/a	n/a
11	RUNX3	chr6:166738819-166739426	GM12878	blood:	n/a	n/a
12	ATF2	chr6:166738758-166739517	GM12878	blood:	n/a	n/a
13	SPI1	chr6:166738794-166739217	GM12891	blood:	n/a	chr6:166739006-166739015
14	MEF2A	chr6:166738779-166739304	GM12878	blood:	n/a	chr6:166739008-166739016
15	SPI1	chr6:166738772-166739236	GM12878	blood:	n/a	chr6:166739006-166739015
16	SP1	chr6:166738776-166739192	GM12878	blood:	n/a	n/a
17	CHD2	chr6:166738865-166739262	GM12878	blood:	n/a	n/a
18	TCF12	chr6:166738856-166739209	GM12878	blood:	n/a	n/a
19	EP300	chr6:166738774-166739582	GM12878	blood:	n/a	chr6:166739110-166739126 chr6:166739006-166739020
20	IRF4	chr6:166738830-166739258	GM12878	blood:	n/a	n/a
21	IKZF1	chr6:166738819-166739090	GM12878	blood:	n/a	chr6:166738869-166738877
22	MTA3	chr6:166738781-166739452	GM12878	blood:	n/a	n/a
23	EBF1	chr6:166738835-166739365	GM12878	blood:	n/a	n/a
24	BHLHE40	chr6:166738792-166739614	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:166738874-166739481	GM12891	blood:	n/a	n/a
26	SPI1	chr6:166738881-166739124	GM12878	blood:	n/a	chr6:166739006-166739015
27	TCF3	chr6:166738814-166739450	GM12878	blood:	n/a	chr6:166738966-166738981
28	SMC3	chr6:166738902-166739279	GM12878	blood:	n/a	n/a
29	MXI1	chr6:166738791-166739594	GM12878	blood:	n/a	n/a
30	SPI1	chr6:166738776-166739237	GM12891	blood:	n/a	chr6:166739006-166739015
31	BCLAF1	chr6:166738692-166739545	GM12878	blood:	n/a	chr6:166739006-166739015
32	SPI1	chr6:166738639-166739576	GM12878	blood:	n/a	chr6:166739006-166739015
33	CUX1	chr6:166738832-166739251	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:
2	chr6:166735098..166738464-chr6:166738723..166741211,4	K562	blood:

Variant related genes	Relation type
SFT2D1	TF binding region
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12209828	0.84[ASN][1000 genomes]
rs2092140	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4318852	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59086118	0.82[EUR][1000 genomes]
rs60636526	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9347122	0.87[EUR][1000 genomes]
rs9355573	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356475	0.87[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	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
2	chr6:166727400-166739000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:166729200-166744200	Weak transcription	Stomach Mucosa	stomach
5	chr6:166729600-166744000	Weak transcription	Small Intestine	intestine
6	chr6:166730400-166740600	Weak transcription	Fetal Kidney	kidney
7	chr6:166730400-166744200	Weak transcription	Fetal Brain Male	brain
8	chr6:166730600-166739000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:166730800-166739000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:166731400-166739000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:166731400-166742800	Strong transcription	Fetal Intestine Small	intestine
12	chr6:166731400-166742800	Strong transcription	Fetal Stomach	stomach
13	chr6:166731600-166739000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:166731600-166743000	Strong transcription	Thymus	Thymus
15	chr6:166731800-166739000	Weak transcription	A549	lung
16	chr6:166731800-166742600	Strong transcription	Placenta	Placenta
17	chr6:166731800-166742800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:166731800-166743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:166731800-166743000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:166731800-166743400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:166732000-166740200	Strong transcription	Fetal Brain Female	brain
22	chr6:166732000-166742800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:166732000-166743000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:166732200-166743000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:166732200-166743000	Strong transcription	Fetal Thymus	thymus
26	chr6:166732200-166743000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr6:166732400-166739000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:166732400-166739000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:166732400-166742800	Strong transcription	Adipose Nuclei	Adipose
30	chr6:166732400-166742800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:166732400-166743000	Strong transcription	Liver	Liver
32	chr6:166732400-166743000	Strong transcription	Dnd41	blood
33	chr6:166732400-166744000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:166732400-166744600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:166732600-166742600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:166732600-166743000	Strong transcription	Primary T cells from cord blood	blood
38	chr6:166732600-166743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:166732800-166743200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:166733000-166739000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:166733000-166743000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:166733200-166739000	Weak transcription	Pancreas	Pancrea
43	chr6:166733200-166744400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
45	chr6:166733400-166739000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:166733400-166742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:166733400-166742800	Strong transcription	Fetal Intestine Large	intestine
48	chr6:166733400-166743000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:166733400-166743000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:166733400-166743400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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