Variant report

Variant	rs6923561
Chromosome Location	chr6:147836282-147836283
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:147834463..147836309-chr6:147844028..147846046,2	K562	blood:
2	chr6:147830521..147832164-chr6:147833225..147837282,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1222119	0.87[CEU][hapmap]
rs1333714	0.93[AFR][1000 genomes]
rs1629209	0.96[AFR][1000 genomes]
rs1631864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1789696	0.89[CEU][hapmap];0.96[AFR][1000 genomes]
rs1789697	0.90[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1789698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1789699	0.96[AFR][1000 genomes]
rs1855374	0.96[AFR][1000 genomes]
rs2780850	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs34292635	0.96[AFR][1000 genomes]
rs471833	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs472577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896920	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs494234	0.87[CEU][hapmap]
rs494395	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs500573	0.96[AFR][1000 genomes]
rs501472	0.96[AFR][1000 genomes]
rs522566	0.96[AFR][1000 genomes]
rs532364	0.95[AFR][1000 genomes]
rs536996	0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs537817	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs538563	0.88[ASW][hapmap];0.87[CEU][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs540384	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs607474	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs609152	0.96[AFR][1000 genomes]
rs609205	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs609963	0.94[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs618181	0.87[CEU][hapmap]
rs623003	0.96[AFR][1000 genomes]
rs623379	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs634979	0.87[CEU][hapmap]
rs636447	0.87[CEU][hapmap]
rs637118	0.95[AFR][1000 genomes]
rs648995	0.87[CEU][hapmap]
rs650375	0.87[CEU][hapmap]
rs655698	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs660814	0.87[CEU][hapmap]
rs666217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66812182	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs669830	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs693879	0.96[AFR][1000 genomes]
rs73020122	0.88[AMR][1000 genomes];0.91[EUR][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	nsv604841	chr6:147832156-148193929	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1020247	chr6:147834097-148478053	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6923561	LTV1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147831400-147836400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:147831400-147838800	Weak transcription	Esophagus	oesophagus
3	chr6:147831600-147852000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:147832000-147839000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:147832400-147836400	Weak transcription	Ovary	ovary
6	chr6:147832400-147844600	Weak transcription	HSMMtube	muscle
7	chr6:147832400-147851200	Weak transcription	Fetal Stomach	stomach
8	chr6:147832400-147851800	Weak transcription	Fetal Kidney	kidney
9	chr6:147832600-147837200	Weak transcription	HSMM	muscle
10	chr6:147832600-147851200	Weak transcription	Fetal Lung	lung
11	chr6:147833000-147844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:147834600-147836600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:147835000-147836600	Weak transcription	Fetal Intestine Large	intestine
14	chr6:147835400-147840200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:147835400-147848200	Weak transcription	Fetal Intestine Small	intestine
16	chr6:147835600-147837000	Enhancers	Colon Smooth Muscle	Colon
17	chr6:147836200-147836600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links