Variant report

Variant	rs12644283
Chromosome Location	chr4:120133549-120133550
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:397)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:397 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr4:120133107-120134612	K562	blood:	n/a	chr4:120134284-120134294
2	POLR2A	chr4:120133076-120134706	A549	lung:	n/a	n/a
3	TAF1	chr4:120133231-120134148	MCF-7	breast:	n/a	n/a
4	HMGN3	chr4:120133366-120134437	K562	blood:	n/a	n/a
5	TEAD4	chr4:120133077-120133854	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZBTB33	chr4:120133138-120133809	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:120133258-120133704	PANC-1	pancreas:	n/a	n/a
8	RCOR1	chr4:120133349-120133879	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:120133325-120134554	GM19193	blood:	n/a	n/a
10	SIN3AK20	chr4:120133360-120133667	HepG2	liver:	n/a	n/a
11	TEAD4	chr4:120133311-120133808	K562	blood:	n/a	n/a
12	HDAC2	chr4:120133364-120133766	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:120133023-120134662	HepG2	liver:	n/a	chr4:120134284-120134294
14	E2F4	chr4:120133181-120134507	MCF10A-Er-Src	breast:	n/a	chr4:120133619-120133630 chr4:120133570-120133581
15	USF2	chr4:120133525-120133852	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:120133186-120134603	K562	blood:	n/a	n/a
17	ELK1	chr4:120133413-120133962	Hela-S3	cervix:	n/a	n/a
18	ZBTB33	chr4:120133024-120134006	HCT-116	colon:	n/a	n/a
19	EP300	chr4:120133220-120133833	A549	lung:	n/a	n/a
20	SIN3A	chr4:120133004-120134727	H1-hESC	embryonic stem cell:	n/a	chr4:120134295-120134303
21	MAX	chr4:120133067-120134753	ECC-1	luminal epithelium:	n/a	chr4:120134284-120134294
22	KAP1	chr4:120133214-120133910	U2OS	brain:	n/a	n/a
23	E2F6	chr4:120133411-120133770	K562	blood:	n/a	n/a
24	MAX	chr4:120133116-120134027	H1-hESC	embryonic stem cell:	n/a	n/a
25	TEAD4	chr4:120133265-120134646	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr4:120132995-120134680	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr4:120133388-120134661	Hela-S3	cervix:	n/a	n/a
28	EP300	chr4:120133367-120133795	T-47D	breast:	n/a	n/a
29	TAF7	chr4:120133156-120134510	H1-hESC	embryonic stem cell:	n/a	n/a
30	STAT3	chr4:120132960-120133917	MCF10A-Er-Src	breast:	n/a	n/a
31	CHD2	chr4:120133187-120133912	GM12878	blood:	n/a	n/a
32	MAFK	chr4:120133344-120134637	K562	blood:	n/a	n/a
33	POLR2A	chr4:120133011-120134696	U87	brain:	n/a	n/a
34	MAFK	chr4:120133390-120133791	HepG2	liver:	n/a	n/a
35	SIN3AK20	chr4:120133229-120133585	A549	lung:	n/a	n/a
36	TAF1	chr4:120133339-120134063	SK-N-SH	brain:	n/a	n/a
37	REST	chr4:120133529-120133735	K562	blood:	n/a	n/a
38	SIN3AK20	chr4:120133187-120134559	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr4:120133015-120134567	K562	blood:	n/a	n/a
40	NFIC	chr4:120133298-120134382	HepG2	liver:	n/a	n/a
41	TAF7	chr4:120133261-120134039	H1-hESC	embryonic stem cell:	n/a	n/a
42	GATA3	chr4:120133286-120133916	MCF-7	breast:	n/a	n/a
43	ZBTB33	chr4:120133395-120133735	HepG2	liver:	n/a	n/a
44	MAX	chr4:120133196-120134676	SK-N-SH	brain:	n/a	chr4:120134284-120134294
45	MAX	chr4:120133070-120134676	ECC-1	luminal epithelium:	n/a	chr4:120134284-120134294
46	POLR2A	chr4:120133082-120134624	HepG2	liver:	n/a	n/a
47	TFAP2C	chr4:120133400-120134572	Hela-S3	cervix:	n/a	chr4:120134252-120134267
48	POLR2A	chr4:120133279-120134427	GM12878	blood:	n/a	n/a
49	POLR2A	chr4:120132974-120134027	HUVEC	blood vessel:	n/a	n/a
50	ATF2	chr4:120133080-120133718	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:120132850..120133665-chr7:1014781..1015295,2	NB4	blood:
2	chr1:116914863..116916593-chr4:120132823..120134505,2	MCF-7	breast:
3	chr4:120107053..120109251-chr4:120131734..120133629,2	MCF-7	breast:
4	chr4:120059391..120062207-chr4:120131058..120133617,2	MCF-7	breast:
5	chr4:120132453..120136158-chr4:120220202..120223113,6	K562	blood:
6	chr4:119988837..119992890-chr4:120132998..120134761,3	MCF-7	breast:
7	chr4:120132319..120136069-chr4:120219720..120222326,6	MCF-7	breast:
8	chr4:119755459..119757778-chr4:120132797..120135484,2	K562	blood:
9	chr4:120132610..120134570-chr4:120221091..120222996,2	MCF-7	breast:
10	chr4:10118096..10120134-chr4:120132938..120134985,2	MCF-7	breast:
11	chr4:120132983..120134127-chr5:40834940..40835540,3	Hela-S3	cervix:
12	chr3:52273199..52273773-chr4:120133265..120133955,2	NB4	blood:
13	chr2:237076560..237077378-chr4:120133405..120134232,2	HCT-116	colon:
14	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
15	chr11:62572491..62573213-chr4:120133328..120134306,3	HCT-116	colon:
16	chr21:27542699..27543375-chr4:120133383..120134375,2	HCT-116	colon:
17	chr11:10830035..10830860-chr4:120133336..120133936,2	HCT-116	colon:
18	chr4:120132950..120135145-chr4:120157017..120160702,4	MCF-7	breast:
19	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
20	chr4:120131661..120133788-chr4:120986266..120989312,3	K562	blood:
21	chr1:28975031..28975543-chr4:120133549..120134385,2	HCT-116	colon:
22	chr4:120133423..120134176-chr6:43603254..43603981,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
USP53	TF binding region
ENSG00000168505	Chromatin interaction
ENSG00000164096	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000273492	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000150961	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000249356	Chromatin interaction
ENSG00000246308	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000142192	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000071127	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000240230	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10518301	0.80[CHD][hapmap]
rs11935130	0.81[CHD][hapmap]
rs11946597	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs12642637	0.88[ASN][1000 genomes]
rs12644226	0.89[ASN][1000 genomes]
rs12645079	0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap]
rs12645965	0.85[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap]
rs17049968	0.85[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap]
rs1858285	0.81[CHD][hapmap]
rs2102541	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833611	0.90[CEU][hapmap]
rs4834761	0.95[ASN][1000 genomes]
rs4834762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834769	1.00[YRI][hapmap]
rs55724227	0.80[ASN][1000 genomes]
rs55732167	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55890361	0.93[ASN][1000 genomes]
rs56034803	0.95[ASN][1000 genomes]
rs56083532	0.93[ASN][1000 genomes]
rs57070054	0.88[ASN][1000 genomes]
rs62326301	0.88[ASN][1000 genomes]
rs62326319	0.88[ASN][1000 genomes]
rs62326320	0.88[ASN][1000 genomes]
rs62326341	0.95[ASN][1000 genomes]
rs62326342	0.95[ASN][1000 genomes]
rs62326344	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62326345	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62326346	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62326347	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62326348	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62326349	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62326352	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328369	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72910519	0.88[ASN][1000 genomes]
rs7694500	0.80[ASN][1000 genomes]
rs7694555	0.80[ASN][1000 genomes]
rs8180225	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12644283	FABP2	cis	cerebellum	SCAN
rs12644283	FABP2	cis	Heart Left Ventricle	GTEx
rs12644283	QRFPR	cis	cerebellum	SCAN
rs12644283	FABP2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120132000-120137000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:120132200-120135400	Active TSS	Psoas Muscle	Psoas
3	chr4:120132200-120136400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:120132400-120134400	Active TSS	Adipose Nuclei	Adipose
5	chr4:120132400-120135200	Active TSS	Left Ventricle	heart
6	chr4:120132400-120135800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr4:120132400-120136200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:120132400-120136200	Active TSS	NH-A	brain
9	chr4:120132400-120136400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:120132400-120136400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr4:120132400-120136400	Active TSS	Stomach Smooth Muscle	stomach
12	chr4:120132400-120137000	Active TSS	Right Ventricle	heart
13	chr4:120132600-120133600	Active TSS	Fetal Stomach	stomach
14	chr4:120132600-120133600	Active TSS	Right Atrium	heart
15	chr4:120132600-120133800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:120132600-120134200	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:120132600-120134400	Active TSS	Fetal Lung	lung
18	chr4:120132600-120134800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:120132600-120134800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:120132600-120135000	Active TSS	Liver	Liver
21	chr4:120132600-120135000	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:120132600-120135200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:120132600-120135200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:120132600-120135400	Active TSS	Duodenum Mucosa	Duodenum
25	chr4:120132600-120135600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr4:120132600-120135600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:120132600-120135600	Active TSS	Brain Anterior Caudate	brain
28	chr4:120132600-120135600	Active TSS	Fetal Intestine Large	intestine
29	chr4:120132600-120135800	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:120132600-120136000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr4:120132600-120136000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:120132600-120136000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:120132600-120136000	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr4:120132600-120136000	Active TSS	Osteobl	bone
35	chr4:120132600-120136200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr4:120132600-120136200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:120132600-120136200	Active TSS	HMEC	breast
38	chr4:120132600-120136600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:120132600-120136600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr4:120132600-120136600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:120132600-120136800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:120132600-120136800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr4:120132600-120136800	Active TSS	NHEK	skin
44	chr4:120132600-120137000	Active TSS	NHDF-Ad	bronchial
45	chr4:120132600-120137200	Active TSS	NHLF	lung
46	chr4:120132600-120137400	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr4:120132600-120138200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:120132800-120133600	Active TSS	Brain Germinal Matrix	brain
49	chr4:120132800-120133600	Bivalent/Poised TSS	Thymus	Thymus
50	chr4:120132800-120134600	Active TSS	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links