Variant report

Variant	rs935007
Chromosome Location	chr2:174041358-174041359
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:174022669..174025027-chr2:174041088..174042876,2	MCF-7	breast:
2	chr2:174034052..174036635-chr2:174040991..174043810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10497402	0.82[CHD][hapmap]
rs11680555	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11687539	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs17710065	0.93[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17710437	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1809139	0.93[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2043950	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358088	0.95[ASN][1000 genomes]
rs3754739	0.91[ASN][1000 genomes]
rs3754747	0.87[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs3769159	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769162	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3769163	0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769173	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769201	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs3820835	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4399689	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4972529	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4972532	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56980119	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59500540	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61264428	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62175824	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6750801	0.90[YRI][hapmap]
rs6759847	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs722864	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs734993	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73974105	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs746179	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567355	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7575319	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7599340	0.94[CEU][hapmap];0.84[GIH][hapmap]
rs7601536	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935006	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs935007	ZAK	Cis_1M	lymphoblastoid	RTeQTL
rs935007	CYBRD1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174015400-174047000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:174016200-174048800	Weak transcription	K562	blood
3	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
4	chr2:174026200-174045000	Weak transcription	Fetal Intestine Small	intestine
5	chr2:174026400-174047600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:174026600-174048800	Weak transcription	Liver	Liver
7	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
8	chr2:174028200-174044200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:174028400-174054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:174030000-174052200	Weak transcription	Fetal Lung	lung
11	chr2:174031200-174046600	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:174032400-174048800	Weak transcription	Dnd41	blood
13	chr2:174037000-174047600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:174037000-174053000	Weak transcription	Right Atrium	heart
15	chr2:174037200-174048400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:174037400-174047600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:174037400-174048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:174037400-174048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:174037400-174048800	Weak transcription	NHEK	skin
20	chr2:174037400-174054600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:174037800-174046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:174038200-174049000	Weak transcription	Left Ventricle	heart
23	chr2:174040400-174046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:174040600-174045800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links