Variant report

Variant	rs10174275
Chromosome Location	chr2:171784493-171784494
allele	C/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	MYBL2	chr2:171784465-171787362	HepG2	liver:	n/a	n/a
2	CBX3	chr2:171784386-171786033	K562	blood:	n/a	n/a
3	SPI1	chr2:171784445-171785176	HL-60	blood:	n/a	n/a
4	MYBL2	chr2:171784460-171787158	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:171784480-171786213	HL-60	blood:	n/a	n/a
6	MBD4	chr2:171784457-171785988	HepG2	liver:	n/a	n/a
7	ELF1	chr2:171784346-171785944	MCF-7	breast:	n/a	chr2:171785740-171785749 chr2:171784757-171784770 chr2:171784816-171784829
8	SIN3A	chr2:171784405-171787135	H1-hESC	embryonic stem cell:	n/a	n/a
9	HCFC1	chr2:171784487-171787614	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr2:171784283-171787953	IMR90	lung:	n/a	n/a
11	POLR2A	chr2:171784453-171787115	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:171784435-171787494	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr2:171784461-171787300	HepG2	liver:	n/a	n/a
14	SPI1	chr2:171784419-171785143	GM12878	blood:	n/a	n/a
15	NFIC	chr2:171784448-171787260	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:171784392-171787423	MCF10A-Er-Src	breast:	n/a	n/a
17	JUN	chr2:171784395-171788550	K562	blood:	n/a	chr2:171784907-171784920
18	SETDB1	chr2:171784441-171785908	U2OS	brain:	n/a	n/a
19	CTCF	chr2:171784405-171787045	A549	lung:	n/a	chr2:171785654-171785667 chr2:171785435-171785444 chr2:171785432-171785450 chr2:171785637-171785650 chr2:171785434-171785455

No.	Distal block	Cell Line	Cell type
1	chr2:171772485..171776882-chr2:171782682..171785818,4	MCF-7	breast:
2	chr2:171784160..171787954-chr2:172288133..172292253,10	K562	blood:
3	chr2:171783060..171786005-chr2:216876902..216878903,2	MCF-7	breast:
4	chr2:171626961..171629009-chr2:171784250..171787377,4	K562	blood:
5	chr2:171774230..171778889-chr2:171780066..171784826,7	K562	blood:
6	chr2:171770723..171773648-chr2:171784124..171786319,2	K562	blood:
7	chr2:171784119..171787322-chr2:172288781..172292051,4	MCF-7	breast:
8	chr2:171783791..171787349-chr2:172286549..172291928,9	K562	blood:
9	chr2:171627023..171629009-chr2:171784250..171786840,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TLK1-3	chr2:171784208-171785364	NONHSAT075436

Variant related genes	Relation type
GORASP2	TF binding region
ENSG00000118242	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000266020	Chromatin interaction
ENSG00000239467	Chromatin interaction
ENSG00000234350	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10168109	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10173304	1.00[EUR][1000 genomes]
rs10204442	1.00[EUR][1000 genomes]
rs10754976	1.00[EUR][1000 genomes]
rs10803856	1.00[EUR][1000 genomes]
rs10930452	1.00[EUR][1000 genomes]
rs12621215	1.00[EUR][1000 genomes]
rs13382924	1.00[EUR][1000 genomes]
rs13385649	1.00[EUR][1000 genomes]
rs13395368	1.00[EUR][1000 genomes]
rs13408916	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13415374	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13417630	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13418838	1.00[EUR][1000 genomes]
rs13422667	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13426912	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13428121	1.00[EUR][1000 genomes]
rs1863773	1.00[EUR][1000 genomes]
rs2033161	1.00[EUR][1000 genomes]
rs2052809	1.00[EUR][1000 genomes]
rs2059722	1.00[EUR][1000 genomes]
rs2217151	1.00[EUR][1000 genomes]
rs2217184	1.00[EUR][1000 genomes]
rs2247657	1.00[EUR][1000 genomes]
rs2356372	1.00[EUR][1000 genomes]
rs2555919	1.00[EUR][1000 genomes]
rs2555920	1.00[EUR][1000 genomes]
rs2555921	1.00[EUR][1000 genomes]
rs2555923	1.00[EUR][1000 genomes]
rs2555924	1.00[EUR][1000 genomes]
rs2555925	1.00[EUR][1000 genomes]
rs2555927	1.00[EUR][1000 genomes]
rs2557800	1.00[EUR][1000 genomes]
rs2557801	1.00[EUR][1000 genomes]
rs2557805	1.00[EUR][1000 genomes]
rs2676129	1.00[EUR][1000 genomes]
rs2676134	1.00[EUR][1000 genomes]
rs2676135	1.00[EUR][1000 genomes]
rs2676146	1.00[EUR][1000 genomes]
rs2676148	1.00[EUR][1000 genomes]
rs2723237	1.00[EUR][1000 genomes]
rs2723244	1.00[EUR][1000 genomes]
rs2723246	1.00[EUR][1000 genomes]
rs2723247	1.00[EUR][1000 genomes]
rs28499279	1.00[EUR][1000 genomes]
rs28641775	1.00[EUR][1000 genomes]
rs4027753	1.00[EUR][1000 genomes]
rs4668366	1.00[EUR][1000 genomes]
rs4668367	1.00[EUR][1000 genomes]
rs6433274	1.00[EUR][1000 genomes]
rs6433279	1.00[EUR][1000 genomes]
rs6433280	1.00[EUR][1000 genomes]
rs6721080	1.00[EUR][1000 genomes]
rs6722314	1.00[EUR][1000 genomes]
rs6732108	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6735986	1.00[EUR][1000 genomes]
rs6749884	1.00[EUR][1000 genomes]
rs6751462	1.00[EUR][1000 genomes]
rs6761606	1.00[EUR][1000 genomes]
rs73027301	1.00[EUR][1000 genomes]
rs7560590	1.00[EUR][1000 genomes]
rs7582081	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs7584937	1.00[EUR][1000 genomes]
rs964171	1.00[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	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10174275	BCHE	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171775000-171784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:171778200-171784800	Weak transcription	Right Ventricle	heart
3	chr2:171778400-171785000	Weak transcription	Right Atrium	heart
4	chr2:171779000-171784600	Weak transcription	Fetal Heart	heart
5	chr2:171781000-171784800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:171781200-171784800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:171781200-171784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:171781200-171784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:171781600-171784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:171783800-171784800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:171783800-171785200	Flanking Active TSS	Dnd41	blood
12	chr2:171784000-171784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:171784400-171784600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr2:171784400-171784600	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:171784400-171784600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:171784400-171784600	Enhancers	Liver	Liver
17	chr2:171784400-171784600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:171784400-171784600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:171784400-171784600	Active TSS	GM12878-XiMat	blood
20	chr2:171784400-171784600	Enhancers	Hela-S3	cervix
21	chr2:171784400-171784600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr2:171784400-171784600	Weak transcription	NHDF-Ad	bronchial
23	chr2:171784400-171784800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:171784400-171784800	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:171784400-171784800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:171784400-171784800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr2:171784400-171784800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:171784400-171784800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:171784400-171784800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:171784400-171784800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:171784400-171784800	Flanking Active TSS	HepG2	liver
32	chr2:171784400-171784800	ZNF genes & repeats	K562	blood
33	chr2:171784400-171785000	Flanking Active TSS	A549	lung
34	chr2:171784400-171785200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:171784400-171785200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr2:171784400-171785200	Flanking Active TSS	HMEC	breast
37	chr2:171784400-171785400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:171784400-171787000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr2:171784400-171787600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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