Variant report

Variant	rs9257316
Chromosome Location	chr6:28849157-28849158
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	chr6:28688047..28690834-chr6:28847432..28849865,2	K562	blood:
2	chr6:28839561..28841445-chr6:28847858..28849885,2	MCF-7	breast:
3	chr6:28841283..28845553-chr6:28846644..28850092,3	MCF-7	breast:
4	chr6:28834738..28837746-chr6:28847549..28850161,3	K562	blood:
5	chr6:28847771..28851189-chr6:28852484..28857224,5	MCF-7	breast:
6	chr6:28848643..28851442-chr6:28923087..28926074,2	K562	blood:
7	chr6:28831527..28833470-chr6:28848530..28850072,2	K562	blood:
8	chr6:28848147..28850932-chr6:28889713..28892018,6	MCF-7	breast:
9	chr6:28848572..28851414-chr6:28862417..28864610,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16897420	0.81[EUR][1000 genomes]
rs2071789	0.81[EUR][1000 genomes]
rs9257260	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257319	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28848000-28849400	Active TSS	Fetal Kidney	kidney
2	chr6:28848000-28849600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28848000-28849600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28848000-28849800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28848200-28849400	Active TSS	Brain Germinal Matrix	brain
6	chr6:28848200-28849600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:28848200-28849600	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:28848200-28849600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:28848200-28849600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:28848200-28850000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:28848400-28849200	Active TSS	Primary T cells from cord blood	blood
12	chr6:28848400-28849200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr6:28848400-28849200	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr6:28848400-28849200	Flanking Active TSS	Fetal Thymus	thymus
15	chr6:28848400-28849200	Active TSS	Rectal Smooth Muscle	rectum
16	chr6:28848400-28849200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
17	chr6:28848400-28849200	Active TSS	HMEC	breast
18	chr6:28848400-28849200	Active TSS	HSMM	muscle
19	chr6:28848400-28849200	Active TSS	NHLF	lung
20	chr6:28848400-28849400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:28848400-28849400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:28848400-28849400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:28848400-28849400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:28848400-28849400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:28848400-28849400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:28848400-28849400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
27	chr6:28848400-28849400	Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:28848400-28849400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:28848400-28849400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:28848400-28849400	Active TSS	Brain Angular Gyrus	brain
31	chr6:28848400-28849400	Active TSS	Brain Cingulate Gyrus	brain
32	chr6:28848400-28849400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr6:28848400-28849400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:28848400-28849400	Active TSS	Fetal Intestine Large	intestine
35	chr6:28848400-28849400	Active TSS	Fetal Intestine Small	intestine
36	chr6:28848400-28849400	Active TSS	Fetal Lung	lung
37	chr6:28848400-28849400	Active TSS	Fetal Muscle Trunk	muscle
38	chr6:28848400-28849400	Active TSS	Fetal Stomach	stomach
39	chr6:28848400-28849400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr6:28848400-28849400	Active TSS	Right Atrium	heart
41	chr6:28848400-28849400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:28848400-28849400	Active TSS	NHEK	skin
43	chr6:28848400-28849400	Active TSS	Osteobl	bone
44	chr6:28848400-28849600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr6:28848400-28849600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:28848400-28849600	Active TSS	H9 Cell Line	embryonic stem cell
47	chr6:28848400-28849600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:28848400-28849600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:28848400-28849600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr6:28848400-28849600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links