Variant report

Variant	rs2230735
Chromosome Location	chr1:9776575-9776576
allele	A/G
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	POLR2A	chr1:9776246-9779771	K562	blood:	n/a	n/a
2	POLR2A	chr1:9775573-9779381	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:9776174-9780433	K562	blood:	n/a	n/a
4	POLR2A	chr1:9776467-9778972	K562	blood:	n/a	n/a
5	POLR2A	chr1:9776542-9779591	K562	blood:	n/a	n/a
6	HMGN3	chr1:9776452-9779534	K562	blood:	n/a	chr1:9779325-9779334 chr1:9779286-9779295
7	POLR2A	chr1:9774413-9778982	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:9776413-9778401	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:9775196-9779517	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:9775202-9779536	K562	blood:	n/a	n/a
11	POLR2A	chr1:9776410-9779516	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
2	chr1:9775370..9777474-chr1:9882453..9884913,2	MCF-7	breast:
3	chr1:9776353..9779413-chr1:9969324..9972333,3	K562	blood:

Variant related genes	Relation type
PIK3CD	TF binding region
ENSG00000231789	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000171608	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28730671	0.83[ASN][1000 genomes]
rs28730674	0.83[ASN][1000 genomes]
rs72633870	0.83[ASN][1000 genomes]
rs72871215	0.83[ASN][1000 genomes]
rs7516129	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 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	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9751000-9777600	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:9751000-9779800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:9761000-9779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:9761000-9781600	Weak transcription	HSMMtube	muscle
6	chr1:9761400-9777200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:9761400-9778000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:9763200-9782400	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:9764600-9777000	Weak transcription	Liver	Liver
10	chr1:9766000-9777200	Weak transcription	HMEC	breast
11	chr1:9766000-9778800	Weak transcription	NHDF-Ad	bronchial
12	chr1:9766000-9779000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:9766000-9779000	Weak transcription	Osteobl	bone
14	chr1:9766200-9779000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
16	chr1:9768800-9777200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:9769200-9783600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:9769600-9777000	Weak transcription	Right Ventricle	heart
19	chr1:9770000-9776800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:9770000-9777000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:9770000-9777000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:9770200-9778800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:9770800-9782600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:9771400-9777600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:9771600-9782600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:9771800-9777200	Weak transcription	Ovary	ovary
27	chr1:9771800-9778800	Weak transcription	NH-A	brain
28	chr1:9772000-9776600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:9772400-9777400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:9772400-9778800	Weak transcription	HSMM	muscle
31	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:9772800-9776600	Enhancers	K562	blood
33	chr1:9773000-9776600	Genic enhancers	Fetal Thymus	thymus
34	chr1:9773200-9778400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr1:9773400-9778800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:9773800-9777000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr1:9774000-9777000	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr1:9774000-9778400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:9774200-9777200	Genic enhancers	Primary B cells from cord blood	blood
40	chr1:9774200-9777400	Genic enhancers	GM12878-XiMat	blood
41	chr1:9774400-9776600	Strong transcription	Lung	lung
42	chr1:9774400-9776600	Genic enhancers	Thymus	Thymus
43	chr1:9774400-9777600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:9774600-9776600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:9774600-9777600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:9774600-9783400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:9774800-9776600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:9774800-9782600	Strong transcription	Brain Germinal Matrix	brain
49	chr1:9775000-9777600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:9775200-9777000	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links