Variant report

Variant	rs2293471
Chromosome Location	chr2:178487729-178487730
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:178487213-178487731	HCT-116	colon:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:178487706-178487756	CMK	blood:	n/a
2	chr2:178487706-178487756	HEEpiC	esophagus:	n/a
3	chr2:178487706-178487756	MCF10A-Er-Src	breast:	n/a
4	chr2:178487706-178487756	NB4	blood:	n/a
5	chr2:178487706-178487756	AG09309	skin:	n/a
6	chr2:178487706-178487756	AG10803	skin:	n/a
7	chr2:178487706-178487756	HMEC	breast:	n/a
8	chr2:178487706-178487756	SK-N-SH_RA	brain:	n/a
9	chr2:178487706-178487756	Hela-S3	cervix:	n/a
10	chr2:178487706-178487756	MCF-7	breast:	n/a
11	chr2:178487706-178487756	Hepatocyte	liver:	n/a
12	chr2:178487706-178487756	HEK293	kidney:	embryo
13	chr2:178487706-178487756	ECC-1	luminal epithelium:	n/a
14	chr2:178487706-178487756	NT2-D1	testis:	n/a
15	chr2:178487706-178487756	HRCEpiC	kidney:	n/a
16	chr2:178487706-178487756	AG09319	gingival:	n/a
17	chr2:178487706-178487756	HCM	heart:	n/a
18	chr2:178487706-178487756	LNCaP	prostate:	n/a
19	chr2:178487706-178487756	AG04449	skin:	fetal
20	chr2:178487706-178487756	IMR90	lung:	fetal
21	chr2:178487706-178487756	PANC-1	pancreas:	n/a
22	chr2:178487706-178487756	NH-A	brain:	n/a
23	chr2:178487706-178487756	T-47D	breast:	n/a
24	chr2:178487706-178487756	ovcar-3	ovarian:	n/a
25	chr2:178487706-178487756	K562	blood:	n/a
26	chr2:178487706-178487756	SKMC	muscle:	n/a
27	chr2:178487706-178487756	U87	brain:	n/a
28	chr2:178487706-178487756	AoSMC	blood vessel:	n/a
29	chr2:178487706-178487756	GM19239	blood:	n/a
30	chr2:178487706-178487756	RPTEC	kidney:	n/a
31	chr2:178487706-178487756	A549	lung:	n/a
32	chr2:178487706-178487756	GM06990	blood:	n/a
33	chr2:178487706-178487756	HCF	heart:	n/a
34	chr2:178487706-178487756	HRPEpiC	eye:	n/a
35	chr2:178487706-178487756	HUVEC	blood vessel:	n/a
36	chr2:178487706-178487756	Caco-2	colon:	n/a
37	chr2:178487706-178487756	HCPEpiC	choroid plexus:	n/a
38	chr2:178487706-178487756	HIPEpiC	eye:	n/a
39	chr2:178487706-178487756	HL-60	blood:	n/a
40	chr2:178487706-178487756	SK-N-MC	brain:	n/a
41	chr2:178487706-178487756	HPAEpiC	pulmonary alveolar:	n/a
42	chr2:178487706-178487756	Jurkat	blood:	n/a
43	chr2:178487706-178487756	GM12878	blood:	n/a
44	chr2:178487706-178487756	AG04450	lung:	fetal
45	chr2:178487706-178487756	NHDF-neo	bronchial:	n/a
46	chr2:178487706-178487756	BE2_C	brain:	n/a
47	chr2:178487706-178487756	SK-N-SH	brain:	n/a
48	chr2:178487706-178487756	SAEC	small airway:	n/a
49	chr2:178487706-178487756	BJ	skin:	n/a
50	chr2:178487706-178487756	HAEpiC	amniotic membrane:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178485267..178487759-chr2:178497863..178500182,2	K562	blood:

No data

Variant related genes	Relation type
TTC30A	TF binding region
TTC30A	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10189303	1.00[JPT][hapmap]
rs10469714	1.00[JPT][hapmap]
rs1047884	0.88[ASW][hapmap];0.90[YRI][hapmap]
rs10497493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11694988	0.85[CEU][hapmap]
rs12618542	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12619506	1.00[JPT][hapmap]
rs12988366	0.85[CEU][hapmap]
rs13000926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13010396	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13014512	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13019660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13034886	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13431105	0.85[CEU][hapmap]
rs1405716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1527398	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1527399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1527400	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap]
rs1527402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1527410	1.00[CHB][hapmap]
rs1534304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544003	1.00[CHB][hapmap]
rs1547580	1.00[CHB][hapmap]
rs1547581	1.00[CHB][hapmap]
rs16865535	0.85[CHD][hapmap]
rs1852530	0.85[CEU][hapmap]
rs1997208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1997209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs2365619	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2886422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3731802	1.00[JPT][hapmap]
rs3813257	0.84[ASN][1000 genomes]
rs4893971	0.85[EUR][1000 genomes]
rs4893972	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4893974	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893975	0.95[CHD][hapmap]
rs4893976	1.00[CHB][hapmap]
rs6705405	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6730406	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734426	0.86[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6734683	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6736390	0.83[YRI][hapmap]
rs7422544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7594290	0.85[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2293471	TTC30B	cis	parietal	SCAN
rs2293471	AGPS	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178484000-178499200	Weak transcription	Pancreas	Pancrea
2	chr2:178484200-178490600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:178484200-178490600	Weak transcription	Fetal Stomach	stomach
4	chr2:178484200-178490800	Weak transcription	Right Atrium	heart
5	chr2:178484400-178490400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:178484400-178490600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:178484400-178490800	Weak transcription	Adipose Nuclei	Adipose
8	chr2:178484400-178490800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:178485400-178490600	Weak transcription	HepG2	liver
10	chr2:178486800-178488000	Enhancers	Brain Germinal Matrix	brain
11	chr2:178487000-178487800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:178487000-178488000	Enhancers	Fetal Kidney	kidney
13	chr2:178487000-178488400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:178487200-178487800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:178487200-178487800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:178487200-178487800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:178487200-178487800	Enhancers	Brain Anterior Caudate	brain
18	chr2:178487200-178487800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:178487200-178488000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:178487200-178488000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:178487400-178487800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:178487400-178487800	Active TSS	Brain Angular Gyrus	brain
23	chr2:178487400-178487800	Active TSS	Brain Hippocampus Middle	brain
24	chr2:178487400-178487800	Enhancers	Fetal Brain Male	brain
25	chr2:178487400-178487800	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:178487400-178488000	Enhancers	Fetal Brain Female	brain
27	chr2:178487600-178487800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr2:178487600-178487800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr2:178487600-178487800	Active TSS	Psoas Muscle	Psoas
30	chr2:178487600-178487800	Enhancers	HUVEC	blood vessel
31	chr2:178487600-178488000	Enhancers	Liver	Liver
32	chr2:178487600-178488000	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr2:178487600-178491200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links