Variant report

Variant	rs6445608
Chromosome Location	chr3:53877233-53877234
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	FOXA1	chr3:53876887-53877258	T-47D	breast:	n/a	n/a
2	REST	chr3:53876715-53877740	HepG2	liver:	n/a	chr3:53876875-53876895 chr3:53876909-53876922 chr3:53876879-53876892 chr3:53876909-53876922
3	WRNIP1	chr3:53876871-53878169	GM12878	blood:	n/a	n/a
4	FOXA2	chr3:53876736-53877673	HepG2	liver:	n/a	n/a
5	RELA	chr3:53876863-53878419	GM19099	blood:	n/a	chr3:53877197-53877206 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
6	FOXA1	chr3:53876281-53877784	HepG2	liver:	n/a	n/a
7	RXRA	chr3:53876797-53877773	HepG2	liver:	n/a	chr3:53877568-53877582 chr3:53877567-53877576
8	RELA	chr3:53876706-53878542	GM12891	blood:	n/a	chr3:53878475-53878484 chr3:53877197-53877206 chr3:53878475-53878484 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
9	EP300	chr3:53876690-53877976	HepG2	liver:	n/a	chr3:53877595-53877604 chr3:53877216-53877230 chr3:53877217-53877231
10	HEY1	chr3:53876036-53880070	HepG2	liver:	n/a	n/a
11	HEY1	chr3:53876129-53880020	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:53877216-53879627	HepG2	liver:	n/a	n/a
13	HNF4A	chr3:53876697-53878028	HepG2	liver:	n/a	chr3:53877532-53877547 chr3:53877568-53877581 chr3:53877568-53877581 chr3:53877568-53877580 chr3:53877567-53877580 chr3:53877568-53877581 chr3:53877799-53877813 chr3:53877565-53877583 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877566-53877581 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877799-53877813 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877136-53877150
14	HNF4G	chr3:53876740-53878019	HepG2	liver:	n/a	chr3:53877532-53877547 chr3:53877568-53877581 chr3:53877568-53877581 chr3:53877568-53877580 chr3:53877567-53877580 chr3:53877568-53877581 chr3:53877799-53877813 chr3:53877565-53877583 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877799-53877813 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877136-53877150
15	POLR2A	chr3:53876086-53880024	HepG2	liver:	n/a	n/a
16	RELA	chr3:53876775-53878205	GM12878	blood:	n/a	chr3:53877197-53877206 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
17	FOXA1	chr3:53876683-53877521	HepG2	liver:	n/a	n/a
18	MAX	chr3:53876216-53877795	HepG2	liver:	n/a	n/a
19	SP1	chr3:53876452-53877907	HepG2	liver:	n/a	chr3:53877064-53877078
20	EP300	chr3:53876734-53877804	HepG2	liver:	n/a	chr3:53877595-53877604 chr3:53877216-53877230 chr3:53877217-53877231
21	ARID3A	chr3:53876698-53878019	HepG2	liver:	n/a	chr3:53877014-53877030
22	POLR2A	chr3:53876459-53880951	HepG2	liver:	n/a	n/a
23	SP1	chr3:53876758-53877299	H1-hESC	embryonic stem cell:	n/a	chr3:53877064-53877078
24	MAZ	chr3:53876750-53877808	HepG2	liver:	n/a	n/a
25	HNF4A	chr3:53876732-53877830	HepG2	liver:	n/a	chr3:53877532-53877547 chr3:53877568-53877581 chr3:53877568-53877581 chr3:53877568-53877580 chr3:53877567-53877580 chr3:53877568-53877581 chr3:53877799-53877813 chr3:53877565-53877583 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877566-53877581 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877799-53877813 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877136-53877150
26	JUND	chr3:53876775-53877328	HepG2	liver:	n/a	n/a
27	HDAC2	chr3:53876695-53877874	HepG2	liver:	n/a	chr3:53877218-53877232 chr3:53877217-53877231 chr3:53877215-53877229 chr3:53876903-53876922 chr3:53877216-53877230
28	POLR2A	chr3:53875240-53880984	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:53876725-53878869	GM19099	blood:	n/a	n/a
30	RCOR1	chr3:53877008-53877428	GM12878	blood:	n/a	n/a
31	MBD4	chr3:53876588-53878155	HepG2	liver:	n/a	n/a
32	TBP	chr3:53876985-53877303	GM12878	blood:	n/a	n/a
33	NR2F2	chr3:53876713-53878089	HepG2	liver:	n/a	chr3:53877564-53877579
34	NFIC	chr3:53876378-53877947	HepG2	liver:	n/a	n/a
35	BRCA1	chr3:53876900-53877389	HepG2	liver:	n/a	n/a
36	CEBPB	chr3:53876851-53877764	HepG2	liver:	n/a	n/a
37	EBF1	chr3:53876510-53878643	GM12878	blood:	n/a	chr3:53878322-53878332 chr3:53877615-53877624 chr3:53877975-53877986 chr3:53878323-53878332
38	EP300	chr3:53876992-53877476	GM12878	blood:	n/a	chr3:53877216-53877230 chr3:53877217-53877231
39	TEAD4	chr3:53876649-53877991	HepG2	liver:	n/a	n/a
40	RELA	chr3:53876690-53878411	GM19193	blood:	n/a	chr3:53876704-53876713 chr3:53876704-53876713 chr3:53877197-53877206 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
41	HDAC2	chr3:53876747-53877317	HepG2	liver:	n/a	chr3:53877218-53877232 chr3:53877217-53877231 chr3:53877215-53877229 chr3:53876903-53876922 chr3:53877216-53877230
42	FOXA2	chr3:53876352-53877780	HepG2	liver:	n/a	n/a
43	FOXA1	chr3:53876748-53877741	HepG2	liver:	n/a	n/a
44	ELF1	chr3:53876753-53877791	HepG2	liver:	n/a	chr3:53877593-53877604
45	ZNF143	chr3:53876715-53877336	GM12878	blood:	n/a	chr3:53876758-53876776
46	MBD4	chr3:53876443-53878220	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:53876293-53881852	HepG2	liver:	n/a	n/a
48	CUX1	chr3:53876998-53877257	GM12878	blood:	n/a	n/a
49	MYBL2	chr3:53876482-53878026	HepG2	liver:	n/a	n/a
50	SP1	chr3:53876879-53877257	GM12878	blood:	n/a	chr3:53877064-53877078

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53871494..53874275-chr3:53875042..53877358,2	MCF-7	breast:
2	chr3:53874777..53878635-chr3:53878874..53882397,7	MCF-7	breast:

Variant related genes	Relation type
IL17RB	TF binding region
ENSG00000056736	Chromatin interaction
ENSG00000016391	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11718497	0.82[CEU][hapmap]
rs13317328	0.85[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs35518479	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445607	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6801605	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv876805	chr3:53865731-53883722	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6445608	CHDH	cis	Nerve Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53852400-53878200	Weak transcription	Hela-S3	cervix
3	chr3:53853800-53879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:53854200-53877400	Weak transcription	Esophagus	oesophagus
6	chr3:53856800-53879200	Weak transcription	Ovary	ovary
7	chr3:53865600-53879800	Weak transcription	Aorta	Aorta
8	chr3:53869600-53879600	Weak transcription	Right Atrium	heart
9	chr3:53870200-53878600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:53870800-53879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:53872800-53877400	Weak transcription	Small Intestine	intestine
12	chr3:53874800-53878000	Enhancers	Fetal Intestine Large	intestine
13	chr3:53875200-53877400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:53875200-53877400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:53875200-53878400	Enhancers	Pancreas	Pancrea
16	chr3:53875200-53878600	Enhancers	Stomach Mucosa	stomach
17	chr3:53875200-53879200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:53875200-53879400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:53875400-53878600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:53875400-53878800	Enhancers	Brain Hippocampus Middle	brain
21	chr3:53875600-53878000	Weak transcription	Gastric	stomach
22	chr3:53875600-53879000	Enhancers	Fetal Intestine Small	intestine
23	chr3:53875600-53879200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:53875600-53879200	Enhancers	Brain Anterior Caudate	brain
25	chr3:53876200-53878600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:53876200-53878600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:53876200-53879200	Enhancers	Brain Angular Gyrus	brain
28	chr3:53876200-53879600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:53876400-53877600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:53876400-53877600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:53876400-53878200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:53876400-53878200	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:53876400-53878800	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:53876400-53878800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr3:53876400-53879000	Enhancers	Brain Substantia Nigra	brain
36	chr3:53876400-53879200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:53876400-53879200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:53876400-53879200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:53876400-53879200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:53876400-53879400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:53876600-53877400	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr3:53876600-53877600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:53876600-53877600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:53876600-53877600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:53876600-53877600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:53876600-53877800	Enhancers	A549	lung
47	chr3:53876600-53878200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:53876600-53879600	Enhancers	Lung	lung
49	chr3:53876800-53877400	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:53876800-53877600	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links