Variant report

Variant	rs2257216
Chromosome Location	chr3:52968726-52968727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52885122..52886033-chr3:52968404..52969074,3	MCF-7	breast:
2	chr3:52879907..52880415-chr3:52968439..52969296,2	K562	blood:
3	chr3:52962197..52966383-chr3:52966982..52969951,4	K562	blood:
4	chr3:52963966..52966247-chr3:52967182..52969951,2	K562	blood:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11130331	0.84[CEU][hapmap];0.98[GIH][hapmap]
rs11922975	0.88[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap]
rs12629687	0.80[AMR][1000 genomes]
rs2245424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2246556	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs2255107	0.86[JPT][hapmap]
rs2336669	0.91[JPT][hapmap]
rs2336670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336672	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439434	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465101	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2564930	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2564947	0.86[JPT][hapmap]
rs2581780	0.86[JPT][hapmap]
rs2581797	0.80[ASN][1000 genomes]
rs2581801	0.86[JPT][hapmap]
rs2581803	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581810	0.91[JPT][hapmap]
rs2581815	0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs2581816	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581819	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2581827	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710313	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2710314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710326	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710339	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2710346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821873	0.85[YRI][hapmap]
rs4515041	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4519686	0.91[JPT][hapmap]
rs4687687	0.80[CEU][hapmap];0.98[GIH][hapmap]
rs6445550	0.91[JPT][hapmap]
rs6768844	0.91[JPT][hapmap]
rs6771610	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs6792578	0.91[JPT][hapmap]
rs6795646	0.82[YRI][hapmap]
rs6799185	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs6801235	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626551	0.80[CEU][hapmap];0.93[YRI][hapmap]
rs7648514	0.89[JPT][hapmap]
rs9311485	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs9810807	0.85[YRI][hapmap]
rs9823697	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846976	0.91[JPT][hapmap]
rs9860296	0.82[YRI][hapmap]
rs9865094	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs9880978	0.87[GIH][hapmap]
rs9985365	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2257216	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2257216	ITIH4-AS1	cis	lung	GTEx
rs2257216	SEMA3G	cis	parietal	SCAN
rs2257216	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2257216	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2257216	ITIH4	cis	cerebellum	SCAN
rs2257216	ITIH4	cis	parietal	SCAN
rs2257216	SFMBT1	cis	cerebellum	SCAN
rs2257216	TEX264	cis	parietal	SCAN
rs2257216	ITIH4	cis	lymphoblastoid	seeQTL
rs2257216	GNL3	cis	cerebellum	SCAN
rs2257216	GNL3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
5	chr3:52932400-52968800	Weak transcription	NHEK	skin
6	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
7	chr3:52949000-52968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
9	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
10	chr3:52954800-52976800	Weak transcription	Brain Germinal Matrix	brain
11	chr3:52955200-52986400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52955800-52968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:52956000-52973800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:52956400-52986400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:52957200-52974800	Weak transcription	Primary T cells from cord blood	blood
16	chr3:52958200-52985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:52960200-52979600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:52961400-52968800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:52961600-52987000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr3:52962400-52969800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:52962400-52969800	Weak transcription	HMEC	breast
22	chr3:52962400-52970000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:52962400-52975800	Weak transcription	HepG2	liver
24	chr3:52962400-52986600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:52962400-52998200	Weak transcription	Lung	lung
26	chr3:52962400-53001600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:52962600-52979400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:52963000-52974800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:52963000-52976400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:52964200-52975600	Weak transcription	Fetal Intestine Small	intestine
33	chr3:52964200-52984400	Weak transcription	Fetal Stomach	stomach
34	chr3:52964200-52995400	Weak transcription	Gastric	stomach
35	chr3:52964400-52968800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:52964400-52976000	Weak transcription	Fetal Intestine Large	intestine
37	chr3:52964400-52984200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:52964400-52988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:52965000-52973600	Weak transcription	Hela-S3	cervix
41	chr3:52965000-52976600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:52965000-52986000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:52965000-52986800	Weak transcription	Thymus	Thymus
44	chr3:52965000-52998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
46	chr3:52965200-52976800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:52965200-52986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:52965400-52969600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:52965400-52973600	Weak transcription	Primary B cells from cord blood	blood
50	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood

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