Variant report

Variant	rs10930579
Chromosome Location	chr2:174075194-174075195
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	MEF2A	chr2:174075150-174075702	K562	blood:	n/a	chr2:174075395-174075410
2	EP300	chr2:174074939-174075815	SK-N-SH	brain:	n/a	n/a
3	SMC3	chr2:174075108-174075821	SK-N-SH	brain:	n/a	n/a
4	FOXA2	chr2:174074924-174075799	A549	lung:	n/a	n/a
5	USF1	chr2:174075077-174075584	K562	blood:	n/a	chr2:174075380-174075391
6	SP1	chr2:174075117-174075780	A549	lung:	n/a	n/a
7	EP300	chr2:174075012-174075711	A549	lung:	n/a	n/a
8	USF1	chr2:174075095-174075633	K562	blood:	n/a	chr2:174075380-174075391
9	USF1	chr2:174075182-174075569	H1-hESC	embryonic stem cell:	n/a	chr2:174075380-174075391
10	NRF1	chr2:174075009-174075695	SK-N-SH	brain:	n/a	n/a
11	USF1	chr2:174075040-174075730	HCT-116	colon:	n/a	chr2:174075380-174075391
12	POLR2A	chr2:174075096-174075620	MCF10A-Er-Src	breast:	n/a	n/a
13	RAD21	chr2:174075144-174075808	ECC-1	luminal epithelium:	n/a	n/a
14	STAT3	chr2:174075192-174075654	MCF10A-Er-Src	breast:	n/a	n/a
15	MEF2A	chr2:174075111-174075730	K562	blood:	n/a	chr2:174075395-174075410
16	RAD21	chr2:174074986-174076222	SK-N-SH	brain:	n/a	n/a
17	USF1	chr2:174075082-174075648	SK-N-SH	brain:	n/a	chr2:174075380-174075391
18	RAD21	chr2:174075114-174075854	MCF-7	breast:	n/a	n/a
19	USF1	chr2:174075138-174075628	A549	lung:	n/a	chr2:174075380-174075391
20	FOXA1	chr2:174075024-174075701	HepG2	liver:	n/a	n/a
21	MEF2A	chr2:174075057-174075702	SK-N-SH	brain:	n/a	chr2:174075395-174075410
22	MAFK	chr2:174075164-174075662	Hela-S3	cervix:	n/a	n/a
23	BHLHE40	chr2:174075154-174075656	K562	blood:	n/a	n/a
24	CEBPB	chr2:174075030-174075648	A549	lung:	n/a	n/a
25	CTCF	chr2:174075070-174075909	HCT-116	colon:	n/a	n/a
26	USF1	chr2:174075101-174075679	HCT-116	colon:	n/a	chr2:174075380-174075391
27	USF1	chr2:174075128-174075541	H1-hESC	embryonic stem cell:	n/a	chr2:174075380-174075391
28	RAD21	chr2:174075147-174075774	HepG2	liver:	n/a	n/a
29	MAFK	chr2:174075096-174075652	IMR90	lung:	n/a	n/a
30	POLR2A	chr2:174075151-174075769	K562	blood:	n/a	n/a
31	CEBPB	chr2:174075084-174075588	A549	lung:	n/a	n/a
32	CBX3	chr2:174075191-174075668	K562	blood:	n/a	n/a
33	USF1	chr2:174075086-174075619	A549	lung:	n/a	chr2:174075380-174075391
34	MEF2A	chr2:174075165-174075859	SK-N-SH	brain:	n/a	chr2:174075395-174075410
35	USF1	chr2:174075152-174075679	ECC-1	luminal epithelium:	n/a	chr2:174075380-174075391
36	RAD21	chr2:174075083-174075879	HCT-116	colon:	n/a	n/a
37	SMC3	chr2:174075154-174075709	Hela-S3	cervix:	n/a	n/a
38	CEBPB	chr2:174074993-174075695	A549	lung:	n/a	n/a
39	SP1	chr2:174074931-174075747	A549	lung:	n/a	n/a
40	RAD21	chr2:174075029-174075823	A549	lung:	n/a	n/a
41	STAT3	chr2:174075067-174075647	MCF10A-Er-Src	breast:	n/a	n/a
42	JUND	chr2:174075068-174075734	SK-N-SH	brain:	n/a	n/a
43	FOSL2	chr2:174075065-174075683	A549	lung:	n/a	n/a
44	CTCF	chr2:174075129-174076180	A549	lung:	n/a	n/a
45	FOXA1	chr2:174074990-174075774	HepG2	liver:	n/a	n/a
46	BCL3	chr2:174074996-174075806	A549	lung:	n/a	n/a
47	USF1	chr2:174075137-174075586	A549	lung:	n/a	chr2:174075380-174075391
48	RFX5	chr2:174075044-174075905	SK-N-SH	brain:	n/a	n/a
49	TCF12	chr2:174074953-174075721	A549	lung:	n/a	n/a
50	USF1	chr2:174075112-174075596	A549	lung:	n/a	chr2:174075380-174075391

No.	Distal block	Cell Line	Cell type
1	chr2:173891857..173892922-chr2:174074727..174076041,13	K562	blood:
2	chr2:173911445..173914009-chr2:174074635..174077598,2	K562	blood:
3	chr2:173892197..173893051-chr2:174074992..174075912,6	MCF-7	breast:
4	chr2:173940105..173940661-chr2:174075014..174075648,2	MCF-7	breast:
5	chr2:173841968..173842672-chr2:174075178..174075788,2	MCF-7	breast:
6	chr2:173941095..173943931-chr2:174073550..174075773,3	MCF-7	breast:
7	chr2:173891912..173892966-chr2:174075041..174076147,6	MCF-7	breast:
8	chr2:173939918..173942569-chr2:174074502..174077579,3	MCF-7	breast:

Variant related genes	Relation type
MLK7-AS1	TF binding region
ENSG00000091436	Chromatin interaction
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12615166	0.83[ASN][1000 genomes]
rs12986917	0.81[ASN][1000 genomes]
rs12987496	0.80[ASN][1000 genomes]
rs12989116	0.81[ASN][1000 genomes]
rs12990553	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997078	0.85[ASN][1000 genomes]
rs12998711	0.83[ASN][1000 genomes]
rs13004212	0.80[ASN][1000 genomes]
rs13008554	0.86[ASN][1000 genomes]
rs13017210	0.82[ASN][1000 genomes]
rs13017438	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029949	0.83[ASN][1000 genomes]
rs13032010	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17302977	0.81[ASN][1000 genomes]
rs17761169	0.85[ASN][1000 genomes]
rs2076857	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289397	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289399	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34472765	0.80[ASN][1000 genomes]
rs34658268	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34702663	0.81[ASN][1000 genomes]
rs35250703	0.80[ASN][1000 genomes]
rs36102078	0.80[ASN][1000 genomes]
rs36103648	0.85[ASN][1000 genomes]
rs3754741	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754743	0.92[ASN][1000 genomes]
rs3754744	0.94[ASN][1000 genomes]
rs3769157	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769161	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769167	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769187	0.94[ASN][1000 genomes]
rs3769192	0.83[ASN][1000 genomes]
rs3769194	0.85[ASN][1000 genomes]
rs4972533	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55913048	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56151459	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56193548	0.80[ASN][1000 genomes]
rs71417423	0.83[ASN][1000 genomes]
rs72905080	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
2	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
4	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
5	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
6	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:174053400-174075600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:174053400-174078400	Weak transcription	Gastric	stomach
9	chr2:174053400-174082000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:174053400-174089800	Weak transcription	Pancreas	Pancrea
11	chr2:174057400-174075800	Weak transcription	Hela-S3	cervix
12	chr2:174058000-174112800	Weak transcription	Spleen	Spleen
13	chr2:174060000-174075200	Weak transcription	Fetal Kidney	kidney
14	chr2:174060200-174092600	Weak transcription	Aorta	Aorta
15	chr2:174061000-174082000	Weak transcription	Fetal Brain Female	brain
16	chr2:174061200-174097600	Weak transcription	Lung	lung
17	chr2:174061400-174092200	Weak transcription	Brain Substantia Nigra	brain
18	chr2:174061600-174077000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:174061600-174083200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:174061600-174083200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:174061800-174075200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:174061800-174080200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:174063600-174075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:174063600-174097600	Weak transcription	HSMM	muscle
25	chr2:174063800-174076200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:174063800-174081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:174063800-174083200	Weak transcription	GM12878-XiMat	blood
28	chr2:174063800-174095000	Weak transcription	Right Ventricle	heart
29	chr2:174064200-174082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:174064200-174083000	Weak transcription	HepG2	liver
31	chr2:174064200-174083400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:174064200-174097600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:174064600-174082000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:174064600-174083200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:174069400-174076000	Weak transcription	Fetal Intestine Large	intestine
36	chr2:174069400-174081800	Weak transcription	Ovary	ovary
37	chr2:174069400-174082200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:174069400-174097000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:174069400-174097600	Weak transcription	Primary B cells from cord blood	blood
40	chr2:174069600-174096600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:174070000-174081800	Weak transcription	Fetal Brain Male	brain
42	chr2:174070400-174075200	Weak transcription	Osteobl	bone
43	chr2:174071200-174075200	Weak transcription	Adipose Nuclei	Adipose
44	chr2:174071400-174076000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:174071600-174075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:174071800-174094200	Weak transcription	Fetal Thymus	thymus
47	chr2:174072000-174078600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:174072200-174095400	Weak transcription	Right Atrium	heart
49	chr2:174073000-174078000	Weak transcription	Brain Germinal Matrix	brain
50	chr2:174073600-174076200	Enhancers	Fetal Heart	heart

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