Variant report

Variant	rs17009978
Chromosome Location	chr10:49496711-49496712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr10:49495811-49496811	MCF-7	breast:	n/a	chr10:49496389-49496399
2	NR2F2	chr10:49495675-49496849	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr10:49495655-49496753	MCF-7	breast:	n/a	n/a
4	ELF1	chr10:49495620-49496728	MCF-7	breast:	n/a	n/a
5	POLR2A	chr10:49495409-49497069	GM12878	blood:	n/a	n/a
6	GATA3	chr10:49495679-49496750	MCF-7	breast:	n/a	n/a
7	SPI1	chr10:49496576-49496836	K562	blood:	n/a	chr10:49496722-49496735 chr10:49496723-49496736
8	GATA3	chr10:49495741-49496883	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49494826..49497610-chr10:49513560..49515926,2	MCF-7	breast:
2	chr10:49496582..49501262-chr10:49513244..49517429,4	K562	blood:
3	chr10:49489462..49491590-chr10:49496144..49498930,2	MCF-7	breast:
4	chr10:49422440..49425186-chr10:49494550..49500073,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225482	TF binding region
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10437450	1.00[AMR][1000 genomes]
rs11101305	1.00[AMR][1000 genomes]
rs11101307	1.00[AMR][1000 genomes]
rs11101308	1.00[AMR][1000 genomes]
rs12252051	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12252584	1.00[AMR][1000 genomes]
rs12253913	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12258885	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12268725	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49492400-49498200	Enhancers	Fetal Thymus	thymus
2	chr10:49493200-49499800	Enhancers	GM12878-XiMat	blood
3	chr10:49493600-49504200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:49494000-49497600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:49494400-49498000	Weak transcription	Adipose Nuclei	Adipose
6	chr10:49494600-49496800	Flanking Active TSS	Dnd41	blood
7	chr10:49495000-49498000	Enhancers	Brain Hippocampus Middle	brain
8	chr10:49495200-49496800	Enhancers	Brain Angular Gyrus	brain
9	chr10:49495200-49497800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr10:49495200-49498200	Enhancers	Brain Substantia Nigra	brain
11	chr10:49495400-49497000	Enhancers	Fetal Stomach	stomach
12	chr10:49495400-49497200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:49495400-49497200	Enhancers	Pancreas	Pancrea
14	chr10:49495400-49497400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr10:49495400-49497800	Enhancers	Brain Cingulate Gyrus	brain
16	chr10:49495400-49498200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr10:49495400-49498800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr10:49495400-49500400	Enhancers	Placenta	Placenta
19	chr10:49495600-49497000	Enhancers	Esophagus	oesophagus
20	chr10:49495600-49497800	Enhancers	Fetal Lung	lung
21	chr10:49495600-49498200	Enhancers	Brain Anterior Caudate	brain
22	chr10:49495600-49498800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr10:49495800-49497200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr10:49495800-49497800	Enhancers	Fetal Muscle Trunk	muscle
25	chr10:49495800-49498200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:49495800-49500400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr10:49496000-49497000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:49496000-49497200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:49496000-49497200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr10:49496200-49497600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:49496200-49497600	Weak transcription	Fetal Brain Male	brain
32	chr10:49496200-49497800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:49496200-49498000	Weak transcription	Fetal Muscle Leg	muscle
34	chr10:49496400-49496800	Enhancers	Duodenum Mucosa	Duodenum
35	chr10:49496400-49497200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr10:49496400-49497200	Weak transcription	Fetal Heart	heart
37	chr10:49496400-49497400	Weak transcription	Fetal Intestine Large	intestine
38	chr10:49496400-49497600	Weak transcription	Stomach Mucosa	stomach
39	chr10:49496400-49497800	Weak transcription	NHEK	skin
40	chr10:49496400-49498000	Weak transcription	Brain Germinal Matrix	brain
41	chr10:49496400-49498800	Weak transcription	Gastric	stomach
42	chr10:49496400-49514200	Weak transcription	Right Atrium	heart
43	chr10:49496600-49496800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr10:49496600-49497000	Weak transcription	HepG2	liver
45	chr10:49496600-49497400	Weak transcription	Colon Smooth Muscle	Colon
46	chr10:49496600-49497600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:49496600-49497600	Weak transcription	Right Ventricle	heart

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