Variant report

Variant	rs2288394
Chromosome Location	chr5:79373803-79373804
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	POLR2A	chr5:79373774-79373817	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
THBS4	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10462572	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs12110039	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.92[ASN][1000 genomes]
rs17878929	0.89[ASN][1000 genomes]
rs2288395	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6891246	0.94[ASN][1000 genomes]
rs6897999	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79351600-79379200	Weak transcription	Pancreas	Pancrea
2	chr5:79352400-79378200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:79354600-79378400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:79359600-79378200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:79360000-79378200	Weak transcription	Brain Angular Gyrus	brain
6	chr5:79361000-79374400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr5:79361400-79378400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:79361600-79378400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:79361800-79378400	Strong transcription	Primary T cells from cord blood	blood
10	chr5:79362600-79377800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:79362600-79378600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:79363000-79378800	Weak transcription	Thymus	Thymus
13	chr5:79364400-79378200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:79365800-79378200	Weak transcription	Fetal Stomach	stomach
15	chr5:79366000-79379000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:79366000-79388000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:79366200-79378200	Weak transcription	Adipose Nuclei	Adipose
18	chr5:79366200-79378400	Weak transcription	Fetal Intestine Small	intestine
19	chr5:79366200-79379000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:79366200-79385000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:79366200-79392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:79366400-79375600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:79366400-79378400	Weak transcription	Liver	Liver
24	chr5:79366400-79378600	Weak transcription	Placenta	Placenta
25	chr5:79366400-79379200	Weak transcription	Spleen	Spleen
26	chr5:79366600-79378200	Weak transcription	Fetal Thymus	thymus
27	chr5:79366600-79378400	Weak transcription	Fetal Kidney	kidney
28	chr5:79366600-79379000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:79366600-79379200	Weak transcription	Lung	lung
30	chr5:79366800-79377600	Weak transcription	Fetal Brain Male	brain
31	chr5:79366800-79377800	Weak transcription	Fetal Brain Female	brain
32	chr5:79366800-79379000	Weak transcription	Primary B cells from cord blood	blood
33	chr5:79367200-79375000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr5:79368400-79374200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:79369000-79378800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr5:79369200-79378600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:79369600-79378600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:79370200-79377600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:79371000-79378200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:79371000-79378400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:79371200-79374000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:79372200-79374600	Strong transcription	Brain Anterior Caudate	brain
43	chr5:79372400-79374600	Weak transcription	K562	blood
44	chr5:79372600-79374000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:79372600-79376400	Strong transcription	Brain Substantia Nigra	brain
46	chr5:79372800-79374000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:79372800-79376200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:79372800-79376400	Strong transcription	Brain Hippocampus Middle	brain
49	chr5:79372800-79378200	Weak transcription	Esophagus	oesophagus
50	chr5:79372800-79378200	Weak transcription	Ovary	ovary

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