Variant report

Variant	rs10204520
Chromosome Location	chr2:172948094-172948095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:172947393-172954021	H1-neurons	neurons:	n/a	n/a
2	REST	chr2:172947161-172968289	H1-neurons	neurons:	n/a	chr2:172949998-172950016 chr2:172955424-172955431 chr2:172966545-172966555 chr2:172949547-172949560 chr2:172949322-172949335 chr2:172959919-172959929 chr2:172964021-172964034 chr2:172963896-172963909 chr2:172957814-172957827 chr2:172966494-172966507 chr2:172954428-172954441 chr2:172955650-172955663 chr2:172963999-172964012 chr2:172959791-172959804 chr2:172955470-172955480 chr2:172955862-172955872 chr2:172967451-172967460 chr2:172959917-172959931
3	POLR2A	chr2:172947263-172954379	H1-neurons	neurons:	n/a	n/a
4	SUZ12	chr2:172946802-172956123	NT2-D1	testis:	n/a	n/a
5	SUZ12	chr2:172944764-172950829	H1-hESC	embryonic stem cell:	n/a	n/a
6	RUNX3	chr2:172947996-172948220	GM12878	blood:	n/a	n/a
7	CTBP2	chr2:172947124-172948254	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:172948073-172948123	PrEC	prostate:	n/a
2	chr2:172948073-172948123	GM12892	blood:	n/a
3	chr2:172948073-172948123	ProgFib	skin:	n/a
4	chr2:172948073-172948123	AG09309	skin:	n/a
5	chr2:172948073-172948123	HCPEpiC	choroid plexus:	n/a
6	chr2:172948073-172948123	NB4	blood:	n/a
7	chr2:172948073-172948123	GM06990	blood:	n/a
8	chr2:172948073-172948123	HIPEpiC	eye:	n/a
9	chr2:172948073-172948123	T-47D	breast:	n/a
10	chr2:172948073-172948123	HRCEpiC	kidney:	n/a
11	chr2:172948073-172948123	U87	brain:	n/a
12	chr2:172948073-172948123	Jurkat	blood:	n/a
13	chr2:172948073-172948123	NHBE	bronchial:	n/a
14	chr2:172948073-172948123	ovcar-3	ovarian:	n/a
15	chr2:172948073-172948123	Caco-2	colon:	n/a
16	chr2:172948073-172948123	HCM	heart:	n/a
17	chr2:172948073-172948123	GM19239	blood:	n/a
18	chr2:172948073-172948123	HCF	heart:	n/a
19	chr2:172948073-172948123	SKMC	muscle:	n/a
20	chr2:172948073-172948123	SK-N-SH	brain:	n/a
21	chr2:172948073-172948123	HPAEpiC	pulmonary alveolar:	n/a
22	chr2:172948073-172948123	HAEpiC	amniotic membrane:	n/a
23	chr2:172948073-172948123	HNPCEpiC	eye:	n/a
24	chr2:172948073-172948123	H1-hESC	embryonic stem cell:	embryo
25	chr2:172948073-172948123	GM12878	blood:	n/a
26	chr2:172948073-172948123	HepG2	liver:	n/a
27	chr2:172948073-172948123	SK-N-MC	brain:	n/a
28	chr2:172948073-172948123	RPTEC	kidney:	n/a
29	chr2:172948073-172948123	BE2_C	brain:	n/a
30	chr2:172948073-172948123	HEEpiC	esophagus:	n/a
31	chr2:172948073-172948123	AG04449	skin:	fetal
32	chr2:172948073-172948123	HEK293	kidney:	embryo
33	chr2:172948073-172948123	AG04450	lung:	fetal
34	chr2:172948073-172948123	HUVEC	blood vessel:	n/a
35	chr2:172948073-172948123	LNCaP	prostate:	n/a
36	chr2:172948073-172948123	CMK	blood:	n/a
37	chr2:172948073-172948123	PFSK-1	brain:	n/a
38	chr2:172948073-172948123	MCF10A-Er-Src	breast:	n/a
39	chr2:172948073-172948123	Hela-S3	cervix:	n/a
40	chr2:172948073-172948123	HMEC	breast:	n/a
41	chr2:172948073-172948123	NH-A	brain:	n/a
42	chr2:172948073-172948123	NHDF-neo	bronchial:	n/a
43	chr2:172948073-172948123	BJ	skin:	n/a
44	chr2:172948073-172948123	K562	blood:	n/a
45	chr2:172948073-172948123	IMR90	lung:	fetal
46	chr2:172948073-172948123	GM12891	blood:	n/a
47	chr2:172948073-172948123	AoSMC	blood vessel:	n/a
48	chr2:172948073-172948123	SAEC	small airway:	n/a
49	chr2:172948073-172948123	HRE	kidney:	n/a
50	chr2:172948073-172948123	MCF-7	breast:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172885280..172887924-chr2:172947289..172951692,6	MCF-7	breast:
2	chr2:172884857..172888115-chr2:172946694..172951424,5	K562	blood:
3	chr2:172863189..172870519-chr2:172946500..172952655,22	K562	blood:
4	chr2:172860607..172867322-chr2:172946572..172954768,24	MCF-7	breast:
5	chr2:172863189..172867097-chr2:172945137..172953576,15	K562	blood:
6	chr2:172920303..172928510-chr2:172947424..172952310,9	K562	blood:
7	chr2:172946999..172948663-chr7:154793329..154795925,2	MCF-7	breast:
8	chr2:172859788..172868192-chr2:172944876..172951443,18	MCF-7	breast:
9	chr2:172776261..172781039-chr2:172946394..172953961,9	K562	blood:

No data

Variant related genes	Relation type
DLX1	TF binding region
DLX1	CpG island
ENSG00000273344	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000128708	Chromatin interaction
ENSG00000157212	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10168377	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12473549	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13390848	1.00[CHB][hapmap]
rs28619352	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172944000-172949200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:172944600-172949400	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr2:172945000-172948200	ZNF genes & repeats	Spleen	Spleen
4	chr2:172945000-172948600	Weak transcription	K562	blood
5	chr2:172945000-172949400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr2:172945000-172949400	Bivalent Enhancer	Fetal Thymus	thymus
7	chr2:172945000-172949600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:172945000-172951400	Enhancers	Pancreas	Pancrea
9	chr2:172945400-172949200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
10	chr2:172945600-172949200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr2:172946000-172949000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
12	chr2:172946000-172949600	Bivalent Enhancer	Stomach Mucosa	stomach
13	chr2:172946200-172948800	Bivalent Enhancer	Adipose Nuclei	Adipose
14	chr2:172946200-172949200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr2:172946400-172953200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
16	chr2:172946800-172948800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
17	chr2:172947000-172949200	Enhancers	HSMMtube	muscle
18	chr2:172947000-172951400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:172947200-172949000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:172947200-172949000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr2:172947200-172949200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:172947200-172949200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr2:172947200-172949200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr2:172947200-172949200	Bivalent Enhancer	HUVEC	blood vessel
25	chr2:172947200-172949400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr2:172947200-172949400	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr2:172947200-172949600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:172947400-172948200	Bivalent Enhancer	Primary T cells from cord blood	blood
29	chr2:172947400-172948200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:172947400-172948200	Bivalent Enhancer	Fetal Stomach	stomach
31	chr2:172947400-172948200	Bivalent Enhancer	Gastric	stomach
32	chr2:172947400-172948200	Bivalent Enhancer	Psoas Muscle	Psoas
33	chr2:172947400-172948400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr2:172947400-172948400	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr2:172947400-172948800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
36	chr2:172947400-172949200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
37	chr2:172947400-172953000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
38	chr2:172947600-172948200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:172947600-172948400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:172947600-172948400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr2:172947600-172948600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:172947600-172948600	Flanking Bivalent TSS/Enh	NHEK	skin
43	chr2:172947600-172949200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
44	chr2:172947600-172949200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:172947600-172949200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:172947600-172949400	Bivalent Enhancer	Placenta	Placenta
47	chr2:172947600-172949800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:172947800-172948200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr2:172947800-172948200	Bivalent Enhancer	Primary B cells from cord blood	blood
50	chr2:172947800-172948200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links