Variant report

Variant	rs1837470
Chromosome Location	chr2:174048371-174048372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:174042344..174044769-chr2:174046655..174049116,2	K562	blood:
2	chr2:174047844..174049361-chr2:174051278..174054008,2	K562	blood:
3	chr2:174047164..174049311-chr2:174061893..174063545,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11680555	1.00[YRI][hapmap]
rs11680612	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687539	0.88[YRI][hapmap]
rs13004345	0.90[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13009008	0.88[ASN][1000 genomes]
rs13030866	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35109796	0.95[ASN][1000 genomes]
rs35339538	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754740	0.84[EUR][1000 genomes]
rs3754747	0.83[LWK][hapmap]
rs3769163	1.00[YRI][hapmap]
rs3769184	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3769185	0.81[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.95[ASN][1000 genomes]
rs4344898	0.81[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.95[ASN][1000 genomes]
rs4972397	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4972534	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722254	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6750801	0.87[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734993	0.94[LWK][hapmap];0.88[YRI][hapmap]
rs7567355	0.82[YRI][hapmap]
rs7575189	0.91[ASW][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8446	0.82[JPT][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1837470	BBS5	cis	cerebellum	SCAN
rs1837470	ZAK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174016200-174048800	Weak transcription	K562	blood
2	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
3	chr2:174026600-174048800	Weak transcription	Liver	Liver
4	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
5	chr2:174028400-174054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:174030000-174052200	Weak transcription	Fetal Lung	lung
7	chr2:174032400-174048800	Weak transcription	Dnd41	blood
8	chr2:174037000-174053000	Weak transcription	Right Atrium	heart
9	chr2:174037200-174048400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:174037400-174048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:174037400-174048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:174037400-174048800	Weak transcription	NHEK	skin
13	chr2:174037400-174054600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:174038200-174049000	Weak transcription	Left Ventricle	heart
15	chr2:174045400-174052800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:174045600-174048800	Weak transcription	HSMM	muscle
17	chr2:174046200-174054200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:174046200-174054400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:174046200-174055800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:174046400-174048600	Weak transcription	Fetal Intestine Large	intestine
21	chr2:174046400-174049400	Weak transcription	Psoas Muscle	Psoas
22	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:174046600-174055800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:174046800-174048400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:174046800-174048800	Weak transcription	Right Ventricle	heart
26	chr2:174046800-174049000	Enhancers	Fetal Heart	heart
27	chr2:174046800-174052800	Weak transcription	Fetal Intestine Small	intestine
28	chr2:174047000-174048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:174047000-174049400	Enhancers	Rectal Smooth Muscle	rectum
30	chr2:174047000-174062800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:174047200-174052600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:174047600-174048400	Enhancers	A549	lung
33	chr2:174047600-174048800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:174047600-174049000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:174047600-174049200	Enhancers	Fetal Stomach	stomach
36	chr2:174047600-174049400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:174047600-174049800	Enhancers	Colon Smooth Muscle	Colon
38	chr2:174047600-174050200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:174047600-174050600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:174047600-174056400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:174047600-174060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:174047600-174062800	Weak transcription	GM12878-XiMat	blood
43	chr2:174047800-174050400	Enhancers	NHLF	lung
44	chr2:174047800-174050600	Enhancers	NHDF-Ad	bronchial
45	chr2:174047800-174050800	Enhancers	Osteobl	bone
46	chr2:174047800-174065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:174048000-174048400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:174048000-174049000	Weak transcription	Hela-S3	cervix
49	chr2:174048200-174048800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:174048200-174049400	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links