Variant report

Variant	rs4470829
Chromosome Location	chr6:166741291-166741292
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	POLR2A	chr6:166736292-166741360	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:

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

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10806847	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10862	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2343590	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4598048	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4709112	0.96[EUR][1000 genomes]
rs6909951	0.92[EUR][1000 genomes]
rs6918901	0.98[EUR][1000 genomes]
rs6927168	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757549	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9355572	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9356476	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356478	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356479	0.90[ASN][1000 genomes]
rs9366005	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366006	0.98[EUR][1000 genomes]
rs9366007	0.98[EUR][1000 genomes]
rs9459654	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4470829	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:166729200-166744200	Weak transcription	Stomach Mucosa	stomach
4	chr6:166729600-166744000	Weak transcription	Small Intestine	intestine
5	chr6:166730400-166744200	Weak transcription	Fetal Brain Male	brain
6	chr6:166731400-166742800	Strong transcription	Fetal Intestine Small	intestine
7	chr6:166731400-166742800	Strong transcription	Fetal Stomach	stomach
8	chr6:166731600-166743000	Strong transcription	Thymus	Thymus
9	chr6:166731800-166742600	Strong transcription	Placenta	Placenta
10	chr6:166731800-166742800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:166731800-166743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:166731800-166743000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:166731800-166743400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:166732000-166742800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr6:166732000-166743000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:166732200-166743000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:166732200-166743000	Strong transcription	Fetal Thymus	thymus
18	chr6:166732200-166743000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:166732400-166742800	Strong transcription	Adipose Nuclei	Adipose
20	chr6:166732400-166742800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:166732400-166743000	Strong transcription	Liver	Liver
22	chr6:166732400-166743000	Strong transcription	Dnd41	blood
23	chr6:166732400-166744000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:166732400-166744600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:166732600-166742600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:166732600-166743000	Strong transcription	Primary T cells from cord blood	blood
28	chr6:166732600-166743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:166732800-166743200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:166733000-166743000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:166733200-166744400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
33	chr6:166733400-166742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:166733400-166742800	Strong transcription	Fetal Intestine Large	intestine
35	chr6:166733400-166743000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:166733400-166743000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:166733400-166743400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:166733600-166742800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:166733600-166743000	Strong transcription	HepG2	liver
40	chr6:166733600-166743400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
42	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
43	chr6:166734200-166742800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:166734200-166742800	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:166734200-166743000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:166734400-166742800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:166734400-166742800	Strong transcription	Osteobl	bone
48	chr6:166734400-166743000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:166734400-166743200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:166734600-166742800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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