Variant report

Variant	rs6692753
Chromosome Location	chr1:174737457-174737458
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174735208..174740631-chr1:174966337..174969324,7	MCF-7	breast:
2	chr1:174737035..174739319-chr1:174960271..174963005,2	K562	blood:
3	chr1:174735393..174743353-chr1:174964672..174971853,16	K562	blood:
4	chr1:174737447..174741477-chr1:174966880..174970168,5	MCF-7	breast:
5	chr1:174735485..174737469-chr1:174955783..174958399,2	K562	blood:
6	chr1:174736386..174740944-chr1:174964309..174969947,11	K562	blood:

Variant related genes	Relation type
ENSG00000252552	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs16847206	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16847237	0.85[CHD][hapmap]
rs2179108	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2179109	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41266052	0.90[EUR][1000 genomes]
rs41498747	1.00[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs4515855	0.85[EUR][1000 genomes]
rs56864802	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57053120	0.81[EUR][1000 genomes]
rs57243929	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57648142	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57898822	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58762254	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59190079	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59354288	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59436654	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60240702	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60665754	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60723087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60865584	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60885521	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61028529	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61329817	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673649	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695956	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700434	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AFR][1000 genomes]
rs6703536	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543502	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv548197	chr1:174731596-174741017	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6692753	dJ383J4.3	cis	multi-tissue	Pritchard
rs6692753	NME7	cis	cerebellum	SCAN
rs6692753	CRYM	trans	lymphoblastoid	RTeQTL
rs6692753		cis	Lymphoblastoid	GTEx
rs6692753	SNORD79	cis	parietal	SCAN
rs6692753	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs6692753	CENPL	cis	lymphoblastoid	seeQTL
rs6692753	C1orf156	cis	parietal	SCAN
rs6692753	SNORD78	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174711800-174745600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174720200-174739000	Weak transcription	GM12878-XiMat	blood
3	chr1:174723200-174739000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:174736000-174737800	Enhancers	Liver	Liver
5	chr1:174736400-174739800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:174737000-174737600	Enhancers	Fetal Intestine Large	intestine
7	chr1:174737000-174737800	Enhancers	Stomach Mucosa	stomach
8	chr1:174737000-174739800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:174737400-174737600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:174737400-174737800	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr1:174737400-174737800	Enhancers	Fetal Muscle Leg	muscle
12	chr1:174737400-174738000	Enhancers	Dnd41	blood
13	chr1:174737400-174738400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:174737400-174738800	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links