Variant report

Variant	rs1840060
Chromosome Location	chr4:86699127-86699128
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	SPI1	chr4:86699120-86700314	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:86699118-86705933	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr4:86698984-86700789	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ARHGAP24	TF binding region

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1377206	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1452679	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16995986	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs2904075	0.82[AFR][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	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86663400-86699800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:86684800-86705600	Weak transcription	Small Intestine	intestine
3	chr4:86695400-86699200	Weak transcription	Gastric	stomach
4	chr4:86695400-86708200	Weak transcription	Pancreas	Pancrea
5	chr4:86695600-86699800	Weak transcription	Right Ventricle	heart
6	chr4:86696000-86699400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:86696000-86703800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:86696200-86699400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:86696400-86699600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:86696400-86699600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:86697000-86699200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:86697000-86699200	Enhancers	NHDF-Ad	bronchial
13	chr4:86697000-86699400	Enhancers	NHLF	lung
14	chr4:86697200-86707800	Weak transcription	Spleen	Spleen
15	chr4:86697400-86699800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr4:86697600-86699400	Weak transcription	Psoas Muscle	Psoas
17	chr4:86697800-86699200	Weak transcription	Fetal Lung	lung
18	chr4:86697800-86699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:86697800-86699400	Weak transcription	NH-A	brain
20	chr4:86697800-86699800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:86697800-86699800	Enhancers	Primary B cells from peripheral blood	blood
22	chr4:86697800-86699800	Weak transcription	Fetal Stomach	stomach
23	chr4:86697800-86699800	Weak transcription	HSMMtube	muscle
24	chr4:86697800-86700200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:86698000-86699200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:86698000-86699200	Weak transcription	A549	lung
27	chr4:86698000-86699400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:86698000-86699400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:86698000-86699400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:86698000-86699400	Weak transcription	Fetal Kidney	kidney
31	chr4:86698000-86699800	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:86698000-86699800	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:86698000-86701800	Weak transcription	Fetal Heart	heart
34	chr4:86698000-86704800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:86698200-86699200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:86698200-86699200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:86698200-86699200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:86698200-86699200	Weak transcription	Adipose Nuclei	Adipose
39	chr4:86698200-86699400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:86698200-86699400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:86698200-86699400	Weak transcription	HSMM	muscle
42	chr4:86698200-86699400	Weak transcription	Osteobl	bone
43	chr4:86698200-86699800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:86698600-86699400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:86698800-86699800	Flanking Active TSS	HUVEC	blood vessel
46	chr4:86699000-86699200	Enhancers	GM12878-XiMat	blood
47	chr4:86699000-86699400	Enhancers	Primary B cells from cord blood	blood
48	chr4:86699000-86699400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links