Variant report

Variant	rs6531980
Chromosome Location	chr4:88282709-88282710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88280472..88283090-chr4:88343390..88345468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170502	Chromatin interaction

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

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

rs_ID	r²[population]
rs12642212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12643799	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531981	0.93[AFR][1000 genomes]
rs6857133	0.80[AFR][1000 genomes]
rs7698689	0.88[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	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 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	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:88256200-88292800	Weak transcription	Gastric	stomach
6	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
7	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
8	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:88258000-88285400	Weak transcription	Small Intestine	intestine
10	chr4:88259200-88283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:88261000-88283200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:88261200-88285000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:88264200-88285600	Weak transcription	Spleen	Spleen
14	chr4:88266200-88285000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:88266400-88292200	Weak transcription	Fetal Brain Male	brain
16	chr4:88266600-88288200	Weak transcription	Brain Germinal Matrix	brain
17	chr4:88267400-88290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:88267400-88308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:88267600-88292400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:88267800-88306000	Weak transcription	Fetal Brain Female	brain
21	chr4:88268000-88292200	Weak transcription	Ovary	ovary
22	chr4:88271200-88298000	Weak transcription	HSMMtube	muscle
23	chr4:88273000-88292200	Weak transcription	Brain Substantia Nigra	brain
24	chr4:88273400-88298800	Weak transcription	Fetal Heart	heart
25	chr4:88273800-88284000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:88274200-88288200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:88274200-88296200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:88274400-88286800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:88274400-88286800	Strong transcription	HepG2	liver
30	chr4:88274400-88296400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr4:88274400-88297000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:88274400-88303400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:88274600-88287200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:88274600-88288000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:88274600-88296200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:88274600-88296400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:88274600-88296600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:88274600-88297200	Strong transcription	Fetal Intestine Large	intestine
39	chr4:88274800-88283200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:88274800-88296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:88274800-88298200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:88275200-88292200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:88275200-88292400	Weak transcription	GM12878-XiMat	blood
44	chr4:88275200-88296200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:88275200-88299400	Strong transcription	Dnd41	blood
46	chr4:88275400-88283200	Weak transcription	Aorta	Aorta
47	chr4:88276000-88284000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr4:88276000-88292400	Weak transcription	NHDF-Ad	bronchial
49	chr4:88276200-88286600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:88276200-88292400	Weak transcription	Muscle Satellite Cultured Cells	--

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