Variant report

Variant	rs2280570
Chromosome Location	chr4:8367142-8367143
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8362353..8364168-chr4:8365634..8367261,2	K562	blood:
2	chr4:8308134..8310233-chr4:8366379..8367956,2	K562	blood:
3	chr4:8348558..8350885-chr4:8366825..8368402,2	MCF-7	breast:
4	chr4:8358055..8360875-chr4:8366726..8369353,3	K562	blood:
5	chr4:8366720..8368366-chr4:8370008..8372883,2	K562	blood:

Variant related genes	Relation type
ENSG00000251615	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10018660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508944	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102851	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103277	1.00[ASN][1000 genomes]
rs13129831	1.00[ASN][1000 genomes]
rs2280569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28690830	0.84[ASN][1000 genomes]
rs34893440	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36074936	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57254469	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824623	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7657076	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv470013	chr4:8315938-8377058	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv878605	chr4:8332057-8378959	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878606	chr4:8349738-8377058	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878607	chr4:8349738-8380857	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv878608	chr4:8349738-8386720	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv461219	chr4:8353829-8390646	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv593637	chr4:8353829-8390646	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	nsv526508	chr4:8357923-8371554	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv966468	chr4:8358228-8374418	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2280570	RP11-774O3.3	cis	lung	GTEx
rs2280570	RP11-774O3.3	cis	Nerve Tibial	GTEx
rs2280570	RP11-774O3.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2280570	LOC285535	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8354400-8367200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr4:8354600-8381000	Weak transcription	Right Atrium	heart
3	chr4:8355800-8384800	Weak transcription	Fetal Lung	lung
4	chr4:8358600-8368200	Weak transcription	Fetal Kidney	kidney
5	chr4:8359000-8367200	Weak transcription	Gastric	stomach
6	chr4:8359800-8371800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:8360400-8394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:8360400-8395600	Weak transcription	NHEK	skin
9	chr4:8362000-8395400	Weak transcription	Fetal Brain Male	brain
10	chr4:8362800-8380200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:8363000-8367200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:8363800-8367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:8363800-8368400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:8363800-8369800	Weak transcription	Psoas Muscle	Psoas
15	chr4:8364000-8383400	Weak transcription	Colonic Mucosa	Colon
16	chr4:8364000-8388600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:8364200-8387000	Weak transcription	Dnd41	blood
18	chr4:8364600-8376800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:8364600-8378200	Weak transcription	NH-A	brain
20	chr4:8364800-8387000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:8364800-8392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:8365000-8372600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:8365000-8382800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:8365000-8385000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:8365200-8385000	Weak transcription	NHLF	lung
26	chr4:8365400-8367400	Weak transcription	HUVEC	blood vessel
27	chr4:8365400-8368200	Strong transcription	Fetal Intestine Large	intestine
28	chr4:8365400-8369000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:8365400-8369800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:8365400-8371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:8365400-8376400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:8365400-8383600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:8365600-8367200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:8365600-8382200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:8365600-8388800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr4:8365800-8383600	Strong transcription	Fetal Stomach	stomach
37	chr4:8366000-8367400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:8366000-8367400	Strong transcription	Primary B cells from cord blood	blood
39	chr4:8366000-8368600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:8366000-8368600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:8366000-8368600	Strong transcription	Brain Angular Gyrus	brain
42	chr4:8366000-8368600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:8366000-8368600	Strong transcription	Esophagus	oesophagus
44	chr4:8366000-8368600	Strong transcription	Fetal Brain Female	brain
45	chr4:8366000-8368800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:8366000-8368800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:8366000-8368800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:8366000-8368800	Strong transcription	Lung	lung
49	chr4:8366000-8369000	Strong transcription	Brain Hippocampus Middle	brain
50	chr4:8366000-8369000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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