Variant report

Variant	rs1409328
Chromosome Location	chr10:6190080-6190081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:6190039-6190691	GM12878	blood:	n/a	n/a
2	ZNF263	chr10:6189811-6190749	HEK293-T-REx	kidney:	n/a	n/a
3	POLR2A	chr10:6189841-6190550	IMR90	lung:	n/a	n/a
4	RUNX3	chr10:6190062-6190825	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:6190072-6190853	HL-60	blood:	n/a	n/a
6	POLR2A	chr10:6189998-6190569	K562	blood:	n/a	n/a
7	POLR2A	chr10:6189970-6190476	K562	blood:	n/a	n/a
8	RUNX3	chr10:6190071-6190816	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6183938..6190482-chr10:6242008..6247032,17	MCF-7	breast:
2	chr10:6189894..6192661-chr10:6244759..6246996,2	MCF-7	breast:
3	chr10:6188903..6191152-chr10:6204778..6206877,2	MCF-7	breast:
4	chr10:6185856..6188791-chr10:6189568..6196117,9	MCF-7	breast:
5	chr10:6148307..6150480-chr10:6188512..6190404,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3155A	TF binding region
RN7SKP78	TF binding region
ENSG00000213994	Chromatin interaction
ENSG00000134453	Chromatin interaction
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10905910	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1409329	0.87[YRI][hapmap]
rs4237413	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4750022	0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7097785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh 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	40 gene(s)	inside rSNPs	diseases
6	nsv894816	chr10:6173416-6190343	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6186400-6190800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr10:6187800-6190800	Weak transcription	NHEK	skin
3	chr10:6188000-6190400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:6188000-6190600	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr10:6188000-6190800	Enhancers	Small Intestine	intestine
6	chr10:6188000-6193200	Weak transcription	Osteobl	bone
7	chr10:6188200-6193200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:6188200-6193200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:6188400-6190200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr10:6188400-6190400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr10:6188400-6190600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:6188400-6190600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
13	chr10:6188400-6191000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:6188400-6191200	Enhancers	Primary B cells from cord blood	blood
15	chr10:6188400-6192800	Weak transcription	Fetal Heart	heart
16	chr10:6188400-6192800	Weak transcription	Ovary	ovary
17	chr10:6188400-6193000	Weak transcription	Brain Substantia Nigra	brain
18	chr10:6188400-6193000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:6188400-6193000	Weak transcription	HUVEC	blood vessel
20	chr10:6188400-6193200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:6188400-6193200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:6188400-6193200	Weak transcription	A549	lung
23	chr10:6188400-6204000	Weak transcription	HSMMtube	muscle
24	chr10:6188400-6225200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:6188600-6190200	Enhancers	Adipose Nuclei	Adipose
26	chr10:6188600-6191200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr10:6188600-6192800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:6188600-6192800	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:6188600-6193000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:6188600-6193000	Weak transcription	Brain Anterior Caudate	brain
31	chr10:6188600-6193000	Weak transcription	Left Ventricle	heart
32	chr10:6188600-6193000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:6188600-6193200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:6188600-6193200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:6188800-6190200	Weak transcription	Thymus	Thymus
36	chr10:6188800-6190200	Enhancers	GM12878-XiMat	blood
37	chr10:6188800-6190400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:6188800-6190400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr10:6188800-6191000	Strong transcription	Fetal Stomach	stomach
40	chr10:6188800-6192800	Weak transcription	Right Ventricle	heart
41	chr10:6188800-6193000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:6188800-6193000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:6188800-6193000	Weak transcription	Colon Smooth Muscle	Colon
44	chr10:6188800-6193000	Weak transcription	NHLF	lung
45	chr10:6188800-6193200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:6189000-6190200	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr10:6189000-6190400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:6189000-6190400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr10:6189000-6190400	Enhancers	Lung	lung
50	chr10:6189000-6190600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links