Variant report

Variant	rs35027728
Chromosome Location	chr6:28056646-28056647
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr6:28056546-28057638	U2OS	brain:	n/a	n/a
2	KAP1	chr6:28056552-28057592	K562	blood:	n/a	n/a
3	SETDB1	chr6:28055578-28058467	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28047399..28050542-chr6:28051923..28057231,4	MCF-7	breast:
2	chr6:28050980..28053789-chr6:28055600..28058077,2	MCF-7	breast:
3	chr6:28049008..28053394-chr6:28054919..28058473,6	MCF-7	breast:
4	chr6:28056458..28058626-chr6:28119915..28122214,2	K562	blood:
5	chr6:28056458..28058352-chr6:28061190..28065331,3	K562	blood:
6	chr6:28047913..28051449-chr6:28052832..28058819,8	K562	blood:
7	chr6:28055848..28058102-chr6:28072977..28074750,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZSCAN12P1	TF binding region
ENSG00000197279	Chromatin interaction
ENSG00000272009	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1564442	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893638	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893731	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893761	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893801	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17767294	0.94[ASN][1000 genomes]
rs2277103	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757186	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59910759	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396575	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400515	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400532	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400551	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049400-28056800	Weak transcription	Aorta	Aorta
2	chr6:28049600-28057000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:28049600-28058600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:28049600-28058600	Weak transcription	Brain Substantia Nigra	brain
5	chr6:28049600-28059200	Weak transcription	Fetal Brain Male	brain
6	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:28049800-28056800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:28049800-28056800	Weak transcription	HSMMtube	muscle
9	chr6:28049800-28057000	Weak transcription	Fetal Heart	heart
10	chr6:28049800-28057600	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:28049800-28058600	Weak transcription	Brain Germinal Matrix	brain
12	chr6:28049800-28058600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:28050000-28056800	Weak transcription	Brain Anterior Caudate	brain
14	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:28051200-28058600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:28053200-28059200	ZNF genes & repeats	Liver	Liver
17	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
18	chr6:28053800-28056800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:28054200-28056800	Weak transcription	Gastric	stomach
20	chr6:28054200-28056800	Weak transcription	Lung	lung
21	chr6:28054200-28058600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:28054200-28058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:28054200-28058600	Weak transcription	Ovary	ovary
24	chr6:28054200-28058600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:28054600-28057200	Strong transcription	Pancreas	Pancrea
26	chr6:28054600-28057800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr6:28054600-28058600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr6:28054800-28056800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:28054800-28058400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr6:28055000-28059200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
31	chr6:28055200-28057600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr6:28055200-28059600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr6:28055400-28057200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
34	chr6:28055400-28057200	Strong transcription	Rectal Smooth Muscle	rectum
35	chr6:28055400-28057200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:28055400-28057400	ZNF genes & repeats	Small Intestine	intestine
37	chr6:28055400-28057400	ZNF genes & repeats	GM12878-XiMat	blood
38	chr6:28055400-28057600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr6:28055400-28057600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:28055400-28057600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
41	chr6:28055400-28057600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:28055400-28057800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
43	chr6:28055400-28058000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:28055400-28058200	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr6:28055400-28058200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
46	chr6:28055400-28058200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
47	chr6:28055400-28058400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:28055400-28058400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
49	chr6:28055400-28058600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:28055400-28058800	ZNF genes & repeats	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links