Variant report

Variant	rs27356
Chromosome Location	chr5:14722441-14722442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14720199..14722691-chr5:14724582..14726482,2	K562	blood:
2	chr5:14720788..14722772-chr5:14725861..14727703,2	MCF-7	breast:
3	chr5:14719915..14722516-chr8:145732826..145735802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167700	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11133794	0.91[ASN][1000 genomes]
rs13189930	0.86[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149493	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs149617	0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs152788	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs153829	0.87[JPT][hapmap]
rs153830	0.87[JPT][hapmap]
rs1875513	0.87[JPT][hapmap];0.89[YRI][hapmap]
rs2455402	0.84[JPT][hapmap]
rs250439	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs250440	0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs258290	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs258374	0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs25945	0.87[JPT][hapmap]
rs25951	0.87[JPT][hapmap]
rs25952	0.87[JPT][hapmap]
rs25983	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs25986	0.93[JPT][hapmap]
rs25987	0.93[JPT][hapmap]
rs25988	0.93[JPT][hapmap]
rs25992	0.93[JPT][hapmap]
rs26307	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs27911	0.93[JPT][hapmap]
rs28004	0.86[JPT][hapmap]
rs31920	0.87[JPT][hapmap]
rs31922	0.87[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs31923	0.87[JPT][hapmap]
rs31925	0.87[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs31926	0.87[JPT][hapmap]
rs31928	0.85[JPT][hapmap]
rs31929	0.87[JPT][hapmap]
rs31930	0.80[JPT][hapmap]
rs31968	0.83[ASW][hapmap];0.87[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42358	0.87[JPT][hapmap]
rs42681	0.84[JPT][hapmap]
rs456180	0.87[JPT][hapmap]
rs466880	0.86[JPT][hapmap]
rs4702043	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs6554856	0.87[JPT][hapmap]
rs6872954	0.80[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs745328	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs95492	0.81[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs27356	DNAH5	cis	parietal	SCAN
rs27356	MMP7	trans	lymphoblastoid	seeQTL
rs27356	FAM105B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14684600-14726200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:14696600-14727600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:14700000-14723800	Weak transcription	Small Intestine	intestine
4	chr5:14710600-14722600	Weak transcription	K562	blood
5	chr5:14711800-14726200	Weak transcription	HSMMtube	muscle
6	chr5:14712400-14726400	Weak transcription	HMEC	breast
7	chr5:14713200-14726400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:14713400-14727400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:14713600-14726000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:14713800-14727400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:14714000-14726200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:14714200-14740800	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:14714400-14722800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:14714400-14727800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:14715000-14725200	Weak transcription	Gastric	stomach
16	chr5:14715000-14744200	Weak transcription	GM12878-XiMat	blood
17	chr5:14715200-14725200	Weak transcription	Aorta	Aorta
18	chr5:14715200-14726200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:14715200-14726200	Weak transcription	HSMM	muscle
20	chr5:14715200-14727600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:14715200-14728400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:14715200-14728600	Weak transcription	Esophagus	oesophagus
23	chr5:14715200-14736200	Weak transcription	Pancreas	Pancrea
24	chr5:14715200-14737400	Weak transcription	Spleen	Spleen
25	chr5:14716000-14722800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr5:14716000-14723200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:14716000-14726000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:14716000-14726000	Weak transcription	Fetal Heart	heart
29	chr5:14716000-14727800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:14716000-14730600	Weak transcription	Fetal Thymus	thymus
31	chr5:14716000-14737000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:14716200-14724600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:14716200-14724600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:14716200-14727400	Weak transcription	Fetal Brain Male	brain
35	chr5:14716400-14723800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:14716400-14726200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:14717000-14725200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:14717000-14727600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:14717000-14727600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:14717200-14724600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:14717200-14725200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:14717200-14725200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:14717200-14725400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:14717200-14727600	Weak transcription	Brain Germinal Matrix	brain
45	chr5:14717200-14728800	Weak transcription	Lung	lung
46	chr5:14717200-14730600	Weak transcription	Ovary	ovary
47	chr5:14717400-14724400	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:14717400-14727400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:14717800-14722800	Weak transcription	Brain Angular Gyrus	brain
50	chr5:14717800-14722800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links