Variant report

Variant	rs9596540
Chromosome Location	chr13:52161231-52161232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr13:52161206-52161296	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr13:52160060..52163108-chr13:52376667..52378456,3	K562	blood:
2	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:
3	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
4	chr13:52022475..52029228-chr13:52156654..52162250,29	K562	blood:
5	chr13:52158311..52160568-chr13:52160634..52165811,6	MCF-7	breast:
6	chr13:52160060..52162638-chr13:52376878..52378456,2	K562	blood:
7	chr13:52025295..52029108-chr13:52160696..52165765,10	K562	blood:

No data

Variant related genes	Relation type
RNY1P6	TF binding region
ENSG00000102796	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10467509	1.00[AMR][1000 genomes]
rs9316549	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9316554	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9591413	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596542	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596546	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9596560	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52157800-52161600	Active TSS	HSMMtube	muscle
2	chr13:52159400-52161400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr13:52159600-52162600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:52159600-52165000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:52159600-52165200	Weak transcription	Gastric	stomach
6	chr13:52159600-52165200	Weak transcription	Small Intestine	intestine
7	chr13:52159600-52170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:52159600-52174600	Weak transcription	Spleen	Spleen
9	chr13:52159800-52161400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:52159800-52161600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:52159800-52162600	Weak transcription	Esophagus	oesophagus
12	chr13:52160000-52161800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr13:52160000-52162600	Weak transcription	Fetal Intestine Large	intestine
14	chr13:52160000-52164200	Weak transcription	Liver	Liver
15	chr13:52160000-52165000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:52160200-52161400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr13:52160200-52161400	Weak transcription	Ovary	ovary
18	chr13:52160200-52161400	Transcr. at gene 5' and 3'	NHEK	skin
19	chr13:52160200-52161600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr13:52160200-52161600	Enhancers	Dnd41	blood
21	chr13:52160200-52161800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr13:52160200-52161800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:52160200-52162200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr13:52160200-52162200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:52160200-52162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr13:52160200-52163200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr13:52160200-52164000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr13:52160200-52164600	Weak transcription	Fetal Heart	heart
29	chr13:52160200-52165000	Weak transcription	Fetal Muscle Leg	muscle
30	chr13:52160200-52165000	Weak transcription	Fetal Stomach	stomach
31	chr13:52160200-52165200	Weak transcription	Fetal Kidney	kidney
32	chr13:52160200-52165200	Weak transcription	Left Ventricle	heart
33	chr13:52160200-52165200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr13:52160200-52165200	Weak transcription	Stomach Mucosa	stomach
35	chr13:52160200-52166000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:52160200-52166600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr13:52160200-52168000	Weak transcription	Pancreas	Pancrea
38	chr13:52160200-52170800	Weak transcription	Fetal Intestine Small	intestine
39	chr13:52160200-52181400	Weak transcription	Thymus	Thymus
40	chr13:52160400-52161400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr13:52160400-52161400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr13:52160400-52161600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr13:52160400-52161800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr13:52160400-52162200	Weak transcription	Adipose Nuclei	Adipose
45	chr13:52160400-52162400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr13:52160400-52162400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr13:52160400-52162400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr13:52160400-52162600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr13:52160400-52162600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:52160400-52162600	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links