Variant report

Variant	rs9003
Chromosome Location	chr1:153516307-153516308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB33	chr1:153516062-153516441	K562	blood:	n/a	n/a
2	POLR2A	chr1:153514448-153518753	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:153516218-153516524	HCT-116	colon:	n/a	n/a
4	SP1	chr1:153516024-153516459	H1-hESC	embryonic stem cell:	n/a	chr1:153516062-153516072
5	POLR2A	chr1:153514113-153518626	PANC-1	pancreas:	n/a	n/a
6	MAZ	chr1:153516288-153516320	K562	blood:	n/a	n/a
7	POLR2A	chr1:153516295-153516572	ProgFib	skin:	n/a	n/a
8	POLR2A	chr1:153516234-153516584	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:153516293-153518722	PANC-1	pancreas:	n/a	n/a
10	REST	chr1:153516088-153516451	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153514799..153517187-chr1:153642186..153644842,2	MCF-7	breast:
2	chr1:153516187..153518294-chr1:153538747..153540345,2	K562	blood:
3	chr1:153511083..153513930-chr1:153515986..153517623,2	K562	blood:
4	chr1:153515859..153517501-chr1:153605058..153607945,2	K562	blood:
5	chr1:153515275..153518447-chr1:153598676..153601896,4	MCF-7	breast:
6	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
7	chr1:153514692..153517082-chr1:153605363..153608061,2	MCF-7	breast:
8	chr1:153514173..153516527-chr1:153537925..153539864,2	K562	blood:
9	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
10	chr1:153513630..153516548-chr17:59476541..59478695,2	MCF-7	breast:
11	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
12	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:

No data

Variant related genes	Relation type
S100A5	TF binding region
ENSG00000272030	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16835344	1.00[AMR][1000 genomes]
rs16835349	1.00[AMR][1000 genomes]
rs16835352	1.00[AMR][1000 genomes]
rs2986203	1.00[AMR][1000 genomes]
rs2986204	1.00[AMR][1000 genomes]
rs2986205	1.00[AMR][1000 genomes]
rs2986207	1.00[AMR][1000 genomes]
rs3006432	1.00[AMR][1000 genomes]
rs3014830	1.00[AMR][1000 genomes]
rs3014844	1.00[AMR][1000 genomes]
rs3014852	1.00[AMR][1000 genomes]
rs3118476	1.00[AMR][1000 genomes]
rs58408424	1.00[AMR][1000 genomes]
rs60387319	1.00[AMR][1000 genomes]
rs73022422	1.00[AMR][1000 genomes]
rs73022487	1.00[AMR][1000 genomes]
rs73022488	1.00[AMR][1000 genomes]
rs73022493	1.00[AMR][1000 genomes]
rs73022495	1.00[AMR][1000 genomes]
rs73024403	1.00[AMR][1000 genomes]
rs73024405	1.00[AMR][1000 genomes]
rs73024413	1.00[AMR][1000 genomes]
rs73024414	1.00[AMR][1000 genomes]
rs73024423	1.00[AMR][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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153509200-153516800	Enhancers	Fetal Thymus	thymus
2	chr1:153509200-153517400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:153509400-153516800	Weak transcription	Right Atrium	heart
4	chr1:153509400-153517000	Weak transcription	HUVEC	blood vessel
5	chr1:153509400-153527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:153509600-153517000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:153511200-153516800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:153511200-153516800	Weak transcription	Pancreas	Pancrea
9	chr1:153511400-153516800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:153511400-153516800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:153511400-153517000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:153511400-153517200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:153511800-153516400	Enhancers	K562	blood
14	chr1:153512000-153517000	Enhancers	Dnd41	blood
15	chr1:153512200-153517200	Enhancers	Thymus	Thymus
16	chr1:153512400-153522400	Enhancers	Stomach Mucosa	stomach
17	chr1:153512800-153516800	Enhancers	Esophagus	oesophagus
18	chr1:153512800-153517000	Enhancers	Placenta	Placenta
19	chr1:153513400-153516800	Weak transcription	Fetal Intestine Large	intestine
20	chr1:153513400-153516800	Weak transcription	Fetal Intestine Small	intestine
21	chr1:153513600-153516400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:153513800-153516400	Weak transcription	Small Intestine	intestine
23	chr1:153513800-153516800	Enhancers	Primary B cells from cord blood	blood
24	chr1:153513800-153516800	Weak transcription	NH-A	brain
25	chr1:153514000-153516400	Weak transcription	Colonic Mucosa	Colon
26	chr1:153514000-153516800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:153514000-153516800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr1:153514000-153516800	Weak transcription	Gastric	stomach
29	chr1:153514000-153517200	Weak transcription	GM12878-XiMat	blood
30	chr1:153514200-153516800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:153514400-153516800	Genic enhancers	Fetal Muscle Leg	muscle
32	chr1:153514400-153517000	Enhancers	HepG2	liver
33	chr1:153514600-153516400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:153514800-153516400	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr1:153514800-153516800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:153514800-153517000	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr1:153514800-153517000	Genic enhancers	Lung	lung
38	chr1:153514800-153517200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:153515000-153516400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:153515000-153516800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:153515000-153516800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:153515000-153516800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:153515000-153517000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:153515000-153517400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:153515000-153517400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
46	chr1:153515000-153518000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:153515200-153516400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:153515200-153516400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:153515200-153516400	Weak transcription	NHEK	skin
50	chr1:153515200-153516800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links