Variant report

Variant	rs28730674
Chromosome Location	chr1:9780196-9780197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9780124..9783096-chr1:9792051..9793928,2	K562	blood:
2	chr1:9647704..9650269-chr1:9779958..9782817,2	K562	blood:
3	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
4	chr1:9774795..9777143-chr1:9779791..9782198,2	MCF-7	breast:
5	chr1:9778823..9786788-chr1:9787182..9791476,8	K562	blood:
6	chr1:9779884..9782063-chr1:9818429..9820131,2	K562	blood:
7	chr1:9778426..9780737-chr1:9796414..9798720,2	K562	blood:

Variant related genes	Relation type
ENSG00000171608	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000231789	Chromatin interaction
ENSG00000188807	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2230735	0.83[ASN][1000 genomes]
rs28730671	1.00[ASN][1000 genomes]
rs28730676	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28730677	0.85[ASN][1000 genomes]
rs4486456	0.92[ASN][1000 genomes]
rs72633870	1.00[ASN][1000 genomes]
rs72871215	1.00[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:115 , 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	chr1:9761000-9781600	Weak transcription	HSMMtube	muscle
3	chr1:9763200-9782400	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
5	chr1:9769200-9783600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:9770800-9782600	Weak transcription	Brain Substantia Nigra	brain
7	chr1:9771600-9782600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:9774600-9783400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:9774800-9782600	Strong transcription	Brain Germinal Matrix	brain
11	chr1:9775400-9782000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:9775600-9783400	Strong transcription	Fetal Brain Female	brain
13	chr1:9776800-9781800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:9777200-9780200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:9777200-9781000	Enhancers	HMEC	breast
16	chr1:9777600-9780200	Genic enhancers	Spleen	Spleen
17	chr1:9777600-9782000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:9777600-9782000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:9777800-9780200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:9777800-9780200	Weak transcription	Ovary	ovary
21	chr1:9777800-9780600	Enhancers	A549	lung
22	chr1:9777800-9781200	Weak transcription	Gastric	stomach
23	chr1:9777800-9790200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:9777800-9790600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:9778000-9781200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:9778000-9782200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:9778200-9780800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:9778200-9782200	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr1:9778200-9782800	Weak transcription	Liver	Liver
30	chr1:9778200-9783400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:9778200-9783400	Weak transcription	Fetal Lung	lung
32	chr1:9778400-9780200	Genic enhancers	Thymus	Thymus
33	chr1:9778400-9781000	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:9778400-9781200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:9778400-9781400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:9778400-9781600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:9778400-9782400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:9778400-9782600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:9778400-9783000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:9778400-9783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:9778400-9793400	Weak transcription	Fetal Kidney	kidney
42	chr1:9778600-9780200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:9778600-9780200	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr1:9778600-9780600	Strong transcription	GM12878-XiMat	blood
45	chr1:9778600-9781200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:9778600-9782000	Genic enhancers	Fetal Thymus	thymus
47	chr1:9778600-9782600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:9778600-9785200	Genic enhancers	Primary T cells from cord blood	blood
49	chr1:9778600-9788400	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr1:9778600-9790600	Weak transcription	Small Intestine	intestine

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