Variant report

Variant	rs1688012
Chromosome Location	chr19:35708031-35708032
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35705153..35708046-chr19:35947064..35948602,2	MCF-7	breast:
2	chr19:35612201..35614910-chr19:35707962..35710691,2	MCF-7	breast:
3	chr19:35633583..35634463-chr19:35707432..35708405,8	MCF-7	breast:
4	chr19:35706486..35711228-chr19:35738412..35741324,6	MCF-7	breast:
5	chr19:35694392..35696589-chr19:35707373..35710054,2	K562	blood:
6	chr19:35658448..35660082-chr19:35706961..35709327,2	K562	blood:
7	chr19:35605173..35607007-chr19:35706718..35709027,2	MCF-7	breast:
8	chr19:35633667..35635767-chr19:35707293..35708391,7	MCF-7	breast:
9	chr19:35707916..35709808-chr19:35710206..35712590,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000089356	Chromatin interaction
ENSG00000105699	Chromatin interaction
ENSG00000221946	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10403023	0.98[ASN][1000 genomes]
rs10425008	0.85[AFR][1000 genomes]
rs10425846	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11084808	0.85[AFR][1000 genomes]
rs12463330	0.84[AFR][1000 genomes]
rs12982723	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1633924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17541474	0.88[CEU][hapmap]
rs17613706	0.94[CEU][hapmap]
rs2188328	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs2214021	0.84[YRI][hapmap];0.88[AFR][1000 genomes]
rs28579145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495570	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498342	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521055	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534481	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538182	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540818	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565818	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247282	0.93[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107155	0.80[AFR][1000 genomes]
rs8182468	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1067541	chr19:35698638-35712439	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2763203	chr19:35700047-35738400	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35694200-35708200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:35698000-35708200	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:35698000-35708200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr19:35701200-35709400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:35705000-35709400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr19:35705200-35708600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:35705200-35709600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:35705200-35711200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:35705400-35709000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:35705400-35711200	Weak transcription	Small Intestine	intestine
11	chr19:35705400-35715200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:35705600-35708600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:35705600-35711400	Weak transcription	Pancreas	Pancrea
14	chr19:35706000-35711200	Weak transcription	Fetal Heart	heart
15	chr19:35706000-35711200	Weak transcription	Fetal Intestine Large	intestine
16	chr19:35706000-35715200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:35707000-35714200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:35707200-35710200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:35707400-35708200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr19:35707400-35708400	ZNF genes & repeats	GM12878-XiMat	blood
21	chr19:35707600-35708200	ZNF genes & repeats	Lung	lung
22	chr19:35707600-35708200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr19:35707800-35708200	Enhancers	Gastric	stomach
24	chr19:35707800-35708200	Enhancers	Stomach Mucosa	stomach
25	chr19:35708000-35708800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr19:35708000-35710400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:35708000-35711200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:35708000-35711200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:35708000-35713600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:35708000-35714400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links