Variant report

Variant	rs1474335
Chromosome Location	chr2:74066461-74066462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74063951..74066600-chr2:74212134..74214083,2	MCF-7	breast:
2	chr2:74066384..74069541-chr2:74082161..74085937,3	K562	blood:
3	chr2:74064765..74066561-chr2:74208554..74211279,2	MCF-7	breast:
4	chr2:74065563..74067367-chr2:74363020..74364872,2	K562	blood:
5	chr2:73907073..73907951-chr2:74066396..74067279,2	MCF-7	breast:
6	chr2:74064367..74067264-chr2:74069235..74073820,5	K562	blood:
7	chr2:74054830..74059575-chr2:74061588..74066831,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255989	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1036113	0.91[CHB][hapmap]
rs12467259	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs13387647	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs13397133	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13411185	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009417	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17009421	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17009424	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17009429	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17009430	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17009433	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17009436	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2070581	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2163539	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2303987	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs35283510	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3738846	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs3813229	0.86[CEU][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs3813232	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4852983	0.86[CEU][hapmap];0.89[GIH][hapmap]
rs59631496	0.93[ASN][1000 genomes]
rs6546875	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6726010	0.80[CHB][hapmap]
rs72814141	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7588498	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594485	0.91[CHB][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	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1474335	ALMS1	cis	parietal	SCAN
rs1474335	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74057000-74069400	Weak transcription	Colonic Mucosa	Colon
2	chr2:74057000-74076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:74057000-74093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:74057600-74071400	Weak transcription	Fetal Kidney	kidney
5	chr2:74058000-74069600	Strong transcription	Primary T cells from cord blood	blood
6	chr2:74058000-74070000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:74058000-74071200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:74058200-74067600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:74058600-74071400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:74058800-74067400	Strong transcription	Liver	Liver
11	chr2:74060000-74071400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:74060000-74072000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:74060400-74067600	Strong transcription	Fetal Thymus	thymus
14	chr2:74060400-74068200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:74060400-74068800	Weak transcription	Small Intestine	intestine
16	chr2:74060400-74071200	Weak transcription	Hela-S3	cervix
17	chr2:74060400-74071600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:74060400-74073000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:74060400-74074200	Weak transcription	Fetal Brain Male	brain
20	chr2:74060400-74076800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:74061000-74068200	Weak transcription	Stomach Mucosa	stomach
22	chr2:74061000-74068600	Weak transcription	Brain Germinal Matrix	brain
23	chr2:74061000-74071400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:74061800-74066600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:74062000-74068800	Weak transcription	Adipose Nuclei	Adipose
26	chr2:74062000-74071600	Weak transcription	Fetal Lung	lung
27	chr2:74062200-74066600	Weak transcription	GM12878-XiMat	blood
28	chr2:74062200-74068600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:74062200-74071400	Weak transcription	NHLF	lung
30	chr2:74062200-74071800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:74062400-74066600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:74062800-74067400	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:74063000-74066800	Weak transcription	HepG2	liver
34	chr2:74063800-74066600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:74063800-74068800	Weak transcription	Pancreas	Pancrea
36	chr2:74063800-74071400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:74064000-74068800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:74064000-74068800	Weak transcription	Gastric	stomach
39	chr2:74064000-74068800	Weak transcription	Ovary	ovary
40	chr2:74064000-74070800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:74064000-74071400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:74064000-74071600	Weak transcription	Left Ventricle	heart
43	chr2:74064000-74071800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:74064000-74071800	Weak transcription	Lung	lung
45	chr2:74064000-74071800	Weak transcription	Thymus	Thymus
46	chr2:74064000-74071800	Weak transcription	Spleen	Spleen
47	chr2:74064000-74072000	Weak transcription	Aorta	Aorta
48	chr2:74064000-74072000	Weak transcription	Right Ventricle	heart
49	chr2:74064000-74072600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:74064000-74074000	Weak transcription	Esophagus	oesophagus

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