Variant report

Variant	rs6508997
Chromosome Location	chr19:42278288-42278289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42274897..42278651-chr19:42287593..42289573,3	MCF-7	breast:
2	chr19:42262778..42266389-chr19:42276917..42279036,3	MCF-7	breast:
3	chr19:42252191..42260165-chr19:42275924..42285275,20	MCF-7	breast:
4	chr19:42208175..42212316-chr19:42277076..42281781,5	MCF-7	breast:
5	chr19:42271676..42273430-chr19:42276461..42278418,2	MCF-7	breast:
6	chr19:42256872..42257731-chr19:42277925..42278830,2	MCF-7	breast:
7	chr19:42277316..42282861-chr19:42295271..42298784,10	MCF-7	breast:
8	chr19:42250551..42264892-chr19:42273965..42282481,23	MCF-7	breast:
9	chr19:42278093..42278816-chr19:42296664..42297371,2	MCF-7	breast:
10	chr19:42146223..42148129-chr19:42277106..42278816,2	MCF-7	breast:
11	chr19:42238849..42240375-chr19:42277307..42280132,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000007306	Chromatin interaction
ENSG00000269354	Chromatin interaction
ENSG00000086548	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10403840	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10408842	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409763	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413359	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11548735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12460461	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12460493	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1971787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2116943	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28547939	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803508	0.84[TSI][hapmap]
rs7258008	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8104232	0.85[EUR][1000 genomes]
rs8105477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3430577	chr19:42247653-42285973	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv911774	chr19:42250325-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3384883	chr19:42253458-42288853	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3319044	chr19:42257039-42297123	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3319045	chr19:42257039-42297123	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2763205	chr19:42258547-42290598	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv911775	chr19:42259228-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6508997	SLC1A5	cis	parietal	SCAN
rs6508997	CEACAM3	cis	multi-tissue	Pritchard
rs6508997	PPP5C	cis	parietal	SCAN
rs6508997	ZNF575	cis	parietal	SCAN
rs6508997	MYPOP	cis	parietal	SCAN
rs6508997	LIG1	cis	parietal	SCAN
rs6508997	PSG3	cis	multi-tissue	Pritchard
rs6508997	CEACAM1	cis	cerebellum	SCAN
rs6508997	PSG9	cis	multi-tissue	Pritchard
rs6508997	EXOC3L2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42274800-42281400	Enhancers	Fetal Intestine Small	intestine
2	chr19:42275200-42281000	Enhancers	Fetal Intestine Large	intestine
3	chr19:42276000-42279800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr19:42276200-42278400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr19:42276200-42278400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr19:42276200-42278400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr19:42276200-42278600	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr19:42276200-42279600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr19:42276200-42282400	Enhancers	Stomach Mucosa	stomach
10	chr19:42276600-42278400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:42276800-42279000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:42276800-42280000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:42276800-42282200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr19:42277000-42279800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:42277200-42280000	Enhancers	Duodenum Mucosa	Duodenum
16	chr19:42277600-42278400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr19:42277600-42279200	Enhancers	Colonic Mucosa	Colon
18	chr19:42277600-42280200	Enhancers	HMEC	breast
19	chr19:42277600-42280400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr19:42277800-42278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:42277800-42280200	Enhancers	NHEK	skin
22	chr19:42278000-42278400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:42278000-42278800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr19:42278000-42278800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr19:42278000-42278800	Enhancers	A549	lung
26	chr19:42278000-42279000	Bivalent Enhancer	Fetal Thymus	thymus
27	chr19:42278000-42279800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:42278000-42279800	Weak transcription	Small Intestine	intestine
29	chr19:42278000-42280200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:42278000-42280200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:42278200-42278400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:42278200-42278600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr19:42278200-42278800	Enhancers	Gastric	stomach
34	chr19:42278200-42279000	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr19:42278200-42281000	Weak transcription	Esophagus	oesophagus

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