Variant report

Variant	rs6660363
Chromosome Location	chr1:9741193-9741194
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	chr1:9736879..9743204-chr1:9743811..9749171,7	K562	blood:
2	chr1:9740675..9742750-chr1:9747291..9749108,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf200-1	chr1:9740770-9741193	ENSG00000231789
2	lnc-C1orf200-1	chr1:9740770-9741193	NONHSAT000814
3	lnc-C1orf200-1	chr1:9740770-9741193	ENSG00000231789.2

Variant related genes	Relation type
ENSG00000171608	Chromatin interaction
ENSG00000231789	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs4240910	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs4333853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4420084	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4488033	0.90[ASN][1000 genomes]
rs4601595	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4846192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4846194	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56338585	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6669509	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9430640	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9430641	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6660363	SRM	cis	cerebellum	SCAN
rs6660363	NMNAT1	cis	parietal	SCAN
rs6660363	PIK3CD	cis	parietal	SCAN
rs6660363	RPL22	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9713200-9744000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:9713200-9747200	Weak transcription	Pancreas	Pancrea
3	chr1:9729600-9746800	Weak transcription	Thymus	Thymus
4	chr1:9732400-9741800	Weak transcription	A549	lung
5	chr1:9732600-9743800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:9734400-9741800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:9734600-9743600	Weak transcription	Fetal Thymus	thymus
8	chr1:9735400-9742000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:9735600-9744200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:9735800-9744200	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr1:9736200-9741200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:9737400-9744400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:9737400-9745800	Weak transcription	K562	blood
14	chr1:9737400-9747000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:9737400-9747200	Weak transcription	Right Atrium	heart
16	chr1:9738200-9741200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:9738200-9746000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:9738600-9741200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:9738600-9742000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:9739000-9744400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:9739000-9747200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:9739200-9741200	Enhancers	GM12878-XiMat	blood
23	chr1:9739400-9742000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:9739800-9744200	Weak transcription	Spleen	Spleen
25	chr1:9739800-9747000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:9739800-9747200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:9740200-9742000	Enhancers	Primary B cells from cord blood	blood
28	chr1:9740400-9741200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:9740400-9741200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:9740400-9743000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:9740400-9744200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:9740400-9747200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:9740600-9741200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:9740800-9741200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:9740800-9741200	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:9740800-9743600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:9740800-9743800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:9741000-9741200	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr1:9741000-9741600	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:9741000-9741800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:9741000-9743600	Weak transcription	Dnd41	blood

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