Variant report

Variant	rs2395617
Chromosome Location	chr6:35285720-35285721
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35275753..35280306-chr6:35283312..35286403,4	MCF-7	breast:
2	chr6:35285639..35286428-chr6:35294982..35295885,2	MCF-7	breast:
3	chr6:35284608..35286901-chr6:35310270..35311991,2	MCF-7	breast:
4	chr6:35285529..35287519-chr6:35436021..35437585,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023892	Chromatin interaction
ENSG00000198755	Chromatin interaction
ENSG00000112033	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs16871749	1.00[GIH][hapmap]
rs16871814	1.00[GIH][hapmap]
rs1929846	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929848	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183834	0.80[EUR][1000 genomes]
rs2234044	1.00[GIH][hapmap]
rs3756856	1.00[GIH][hapmap]
rs4713842	0.80[EUR][1000 genomes]
rs4713843	0.80[EUR][1000 genomes]
rs4713844	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457815	1.00[CHB][hapmap]
rs6906666	1.00[GIH][hapmap]
rs6919534	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931442	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937124	1.00[CHB][hapmap]
rs707969	0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs729925	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734538	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763155	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763157	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751726	1.00[CHB][hapmap]
rs7767150	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770619	1.00[CHB][hapmap]
rs9394282	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462081	1.00[CHB][hapmap]
rs9658077	1.00[CHB][hapmap]
rs9658081	1.00[CHB][hapmap]
rs9658085	1.00[CHB][hapmap]
rs9658119	1.00[CHB][hapmap]
rs9658151	1.00[CHB][hapmap]

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	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
4	nsv602907	chr6:35285720-35312267	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2395617	TCP11	cis	lymphoblastoid	seeQTL
rs2395617	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35276000-35293800	Weak transcription	K562	blood
2	chr6:35280800-35293200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:35281000-35285800	Weak transcription	NHEK	skin
4	chr6:35281600-35291600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr6:35282000-35293400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:35282000-35293600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:35282000-35293800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:35282200-35293600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:35282600-35293600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:35282800-35293600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:35283400-35293400	Strong transcription	Primary B cells from cord blood	blood
12	chr6:35283800-35293400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:35284000-35285800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:35284000-35291600	Strong transcription	Dnd41	blood
15	chr6:35284000-35293000	Strong transcription	Primary T cells from cord blood	blood
16	chr6:35284000-35293400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:35284200-35286000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:35284200-35290800	Strong transcription	GM12878-XiMat	blood
19	chr6:35284200-35293400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:35284400-35292800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:35284400-35293600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:35284800-35290600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:35285200-35286000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:35285200-35286000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:35285200-35286000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:35285200-35286600	Active TSS	Brain Anterior Caudate	brain
27	chr6:35285200-35286800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr6:35285200-35286800	Active TSS	A549	lung
29	chr6:35285200-35290800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:35285200-35292800	Strong transcription	Thymus	Thymus
31	chr6:35285400-35285800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:35285400-35285800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr6:35285400-35285800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:35285400-35285800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr6:35285400-35285800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
36	chr6:35285400-35285800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:35285400-35285800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:35285400-35285800	Enhancers	Liver	Liver
39	chr6:35285400-35285800	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr6:35285400-35285800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:35285400-35285800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:35285400-35285800	Flanking Active TSS	Fetal Heart	heart
43	chr6:35285400-35285800	Enhancers	Gastric	stomach
44	chr6:35285400-35285800	Flanking Active TSS	HepG2	liver
45	chr6:35285400-35286000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
46	chr6:35285400-35286000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
47	chr6:35285400-35286000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr6:35285400-35286000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr6:35285400-35286000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr6:35285400-35286000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links