Variant report

Variant	rs12649929
Chromosome Location	chr4:152217433-152217434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr4:152217369-152217734	HepG2	liver:	n/a	chr4:152217652-152217664 chr4:152217648-152217660 chr4:152217656-152217668
2	FOXA1	chr4:152217377-152217679	HepG2	liver:	n/a	chr4:152217652-152217664 chr4:152217648-152217660 chr4:152217656-152217668
3	FOXA2	chr4:152217416-152217689	HepG2	liver:	n/a	chr4:152217652-152217664 chr4:152217648-152217660 chr4:152217656-152217668
4	RFX5	chr4:152217371-152217682	HepG2	liver:	n/a	n/a
5	FOXA1	chr4:152217362-152217677	HepG2	liver:	n/a	chr4:152217652-152217664 chr4:152217648-152217660 chr4:152217656-152217668

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:152217416-152217466	HPAEpiC	pulmonary alveolar:	n/a
2	chr4:152217416-152217466	CMK	blood:	n/a
3	chr4:152217416-152217466	HAEpiC	amniotic membrane:	n/a
4	chr4:152217416-152217466	T-47D	breast:	n/a
5	chr4:152217416-152217466	GM06990	blood:	n/a
6	chr4:152217416-152217466	SKMC	muscle:	n/a
7	chr4:152217416-152217466	NB4	blood:	n/a
8	chr4:152217416-152217466	AoSMC	blood vessel:	n/a
9	chr4:152217416-152217466	HCM	heart:	n/a
10	chr4:152217416-152217466	A549	lung:	n/a
11	chr4:152217416-152217466	AG10803	skin:	n/a
12	chr4:152217416-152217466	MCF-7	breast:	n/a
13	chr4:152217416-152217466	GM12892	blood:	n/a
14	chr4:152217416-152217466	GM12878	blood:	n/a
15	chr4:152217416-152217466	HCPEpiC	choroid plexus:	n/a
16	chr4:152217416-152217466	K562	blood:	n/a
17	chr4:152217416-152217466	Hela-S3	cervix:	n/a
18	chr4:152217416-152217466	HEK293	kidney:	embryo
19	chr4:152217416-152217466	RPTEC	kidney:	n/a
20	chr4:152217416-152217466	IMR90	lung:	fetal
21	chr4:152217416-152217466	NHDF-neo	bronchial:	n/a
22	chr4:152217416-152217466	NHBE	bronchial:	n/a
23	chr4:152217416-152217466	AG04450	lung:	fetal
24	chr4:152217416-152217466	SK-N-MC	brain:	n/a
25	chr4:152217416-152217466	HIPEpiC	eye:	n/a
26	chr4:152217416-152217466	HRE	kidney:	n/a
27	chr4:152217416-152217466	Jurkat	blood:	n/a
28	chr4:152217416-152217466	U87	brain:	n/a
29	chr4:152217416-152217466	GM12891	blood:	n/a
30	chr4:152217416-152217466	AG09309	skin:	n/a
31	chr4:152217416-152217466	ProgFib	skin:	n/a
32	chr4:152217416-152217466	GM19239	blood:	n/a
33	chr4:152217416-152217466	SK-N-SH_RA	brain:	n/a
34	chr4:152217416-152217466	AG09319	gingival:	n/a
35	chr4:152217416-152217466	SAEC	small airway:	n/a
36	chr4:152217416-152217466	HMEC	breast:	n/a
37	chr4:152217416-152217466	H1-hESC	embryonic stem cell:	embryo
38	chr4:152217416-152217466	AG04449	skin:	fetal
39	chr4:152217416-152217466	HCF	heart:	n/a
40	chr4:152217416-152217466	HEEpiC	esophagus:	n/a
41	chr4:152217416-152217466	MCF10A-Er-Src	breast:	n/a
42	chr4:152217416-152217466	ECC-1	luminal epithelium:	n/a
43	chr4:152217416-152217466	BE2_C	brain:	n/a
44	chr4:152217416-152217466	NH-A	brain:	n/a
45	chr4:152217416-152217466	SK-N-SH	brain:	n/a
46	chr4:152217416-152217466	HNPCEpiC	eye:	n/a
47	chr4:152217416-152217466	PFSK-1	brain:	n/a
48	chr4:152217416-152217466	PrEC	prostate:	n/a
49	chr4:152217416-152217466	HL-60	blood:	n/a
50	chr4:152217416-152217466	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152215556..152217545-chr4:152227958..152229723,3	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-1282P	TF binding region
RNU6-1282P	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12647331	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13102005	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13112985	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13117723	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13120319	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13126069	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13126943	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128346	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13135328	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13137979	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13148086	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13150868	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316858	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17590612	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34041707	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36097019	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3990734	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4385037	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66559303	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819551	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6846745	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152196000-152218400	Weak transcription	Psoas Muscle	Psoas
2	chr4:152197800-152242400	Weak transcription	Aorta	Aorta
3	chr4:152198800-152221800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:152198800-152242800	Weak transcription	Fetal Lung	lung
5	chr4:152201600-152228600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:152203600-152243000	Weak transcription	Esophagus	oesophagus
7	chr4:152206400-152225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:152206800-152225400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:152208400-152228400	Weak transcription	Fetal Stomach	stomach
10	chr4:152212800-152225400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:152213000-152234800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:152213400-152218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:152213400-152223200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:152213400-152224800	Weak transcription	HMEC	breast
15	chr4:152213400-152225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:152213400-152228400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:152213400-152235800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:152213600-152221800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:152214000-152218200	Weak transcription	HUVEC	blood vessel
20	chr4:152214800-152219000	Enhancers	Brain Angular Gyrus	brain
21	chr4:152215000-152217600	Enhancers	Brain Substantia Nigra	brain
22	chr4:152215000-152218000	Enhancers	Fetal Heart	heart
23	chr4:152215000-152218200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:152215200-152218600	Weak transcription	Brain Anterior Caudate	brain
25	chr4:152215600-152217600	Enhancers	Small Intestine	intestine
26	chr4:152215600-152218800	Enhancers	Liver	Liver
27	chr4:152216000-152217800	Enhancers	Fetal Intestine Small	intestine
28	chr4:152216000-152218600	Enhancers	Stomach Mucosa	stomach
29	chr4:152216200-152217800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:152216200-152217800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:152216200-152218800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:152216400-152217600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr4:152216400-152217600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:152216400-152217800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:152216400-152219000	Enhancers	Brain Hippocampus Middle	brain
36	chr4:152216400-152223000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:152216400-152224800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:152216400-152224800	Weak transcription	Ovary	ovary
39	chr4:152216600-152217600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:152216600-152217800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr4:152216600-152217800	Enhancers	Duodenum Mucosa	Duodenum
42	chr4:152216600-152218400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:152216600-152218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:152216600-152218600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:152216600-152219000	Weak transcription	Left Ventricle	heart
46	chr4:152216600-152219200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr4:152216600-152224800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:152216600-152224800	Weak transcription	NHEK	skin
49	chr4:152216600-152225800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr4:152216600-152228600	Weak transcription	H9 Cell Line	embryonic stem cell

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