Variant report

Variant	rs4316697
Chromosome Location	chr15:49729925-49729926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49725074..49727575-chr15:49729754..49732009,2	K562	blood:

Variant related genes	Relation type
ENSG00000140285	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10467992	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10519230	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs10851475	0.81[CEU][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap]
rs10851476	0.80[JPT][hapmap]
rs11070687	0.80[JPT][hapmap]
rs11070692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070693	1.00[ASW][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs11631040	0.89[ASW][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs11636795	0.86[YRI][hapmap]
rs11638378	0.87[AFR][1000 genomes]
rs11852524	0.82[ASW][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap];0.91[YRI][hapmap]
rs11854667	0.80[JPT][hapmap]
rs11858114	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[MEX][hapmap]
rs12439429	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12439479	0.89[AFR][1000 genomes]
rs12900001	0.85[GIH][hapmap]
rs12909779	0.80[JPT][hapmap]
rs12913745	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs12916840	0.80[JPT][hapmap]
rs1429556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16962243	0.81[GIH][hapmap]
rs16962440	0.90[CHB][hapmap]
rs16962486	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962490	1.00[ASW][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs1816293	0.80[JPT][hapmap]
rs1904316	0.90[CHB][hapmap]
rs1904317	0.90[ASW][hapmap]
rs2086256	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[MEX][hapmap]
rs2127241	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2127242	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[MEX][hapmap]
rs2163095	0.80[JPT][hapmap]
rs2163096	0.80[JPT][hapmap]
rs2219812	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[MEX][hapmap]
rs2580926	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4421927	0.80[JPT][hapmap]
rs520949	0.82[ASW][hapmap]
rs6493361	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs6493363	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap]
rs6493369	0.92[GIH][hapmap]
rs7162360	0.80[JPT][hapmap]
rs7179237	0.80[JPT][hapmap]
rs735495	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs754165	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs754166	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs8024102	0.80[JPT][hapmap]
rs8025952	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs8031892	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040075	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs919447	0.80[JPT][hapmap]
rs981612	0.80[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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4316697	DTWD1	cis	cerebellum	SCAN
rs4316697	DTWD1	Cis_1M	lymphoblastoid	RTeQTL
rs4316697	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs4316697	DTWD1	cis	lymphoblastoid	seeQTL
rs4316697	MAP1A	cis	cerebellum	SCAN
rs4316697	CATSPER2P1	cis	cerebellum	SCAN
rs4316697	SPATA5L1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716200-49732200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:49718000-49731200	Weak transcription	Left Ventricle	heart
4	chr15:49719400-49731200	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
6	chr15:49721800-49730000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:49725400-49731000	Weak transcription	Brain Substantia Nigra	brain
8	chr15:49725400-49733800	Enhancers	Rectal Smooth Muscle	rectum
9	chr15:49726200-49732800	Enhancers	Fetal Heart	heart
10	chr15:49726800-49731200	Weak transcription	Ovary	ovary
11	chr15:49727000-49730400	Enhancers	Colon Smooth Muscle	Colon
12	chr15:49728200-49732400	Enhancers	Fetal Stomach	stomach
13	chr15:49728400-49730000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:49728400-49730400	Enhancers	NHLF	lung
15	chr15:49728800-49731200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:49729000-49731200	Enhancers	Osteobl	bone
17	chr15:49729000-49731400	Weak transcription	Fetal Kidney	kidney
18	chr15:49729000-49733200	Weak transcription	HSMMtube	muscle
19	chr15:49729200-49730000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:49729200-49730000	Weak transcription	NHDF-Ad	bronchial
21	chr15:49729200-49731000	Weak transcription	Fetal Lung	lung
22	chr15:49729200-49731200	Weak transcription	HSMM	muscle
23	chr15:49729200-49731400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:49729400-49730000	Enhancers	NH-A	brain
25	chr15:49729400-49730200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr15:49729600-49730000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:49729600-49730800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr15:49729800-49730200	Enhancers	Adipose Nuclei	Adipose
29	chr15:49729800-49731200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:49729800-49731200	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links