Variant report

Variant	rs28887326
Chromosome Location	chr7:66170940-66170941
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	chr7:66163629..66166262-chr7:66168489..66172112,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10234018	0.82[EUR][1000 genomes]
rs10252765	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10272546	0.81[ASN][1000 genomes]
rs10274773	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1110414	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11772264	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11772636	0.81[EUR][1000 genomes]
rs11773829	0.82[EUR][1000 genomes]
rs1553609	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1553610	0.80[EUR][1000 genomes]
rs1860468	0.81[ASN][1000 genomes]
rs1860470	0.81[ASN][1000 genomes]
rs1961155	0.80[EUR][1000 genomes]
rs2003301	0.82[EUR][1000 genomes]
rs2191268	0.81[ASN][1000 genomes]
rs2286683	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286684	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2420824	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2420827	0.81[ASN][1000 genomes]
rs2659889	0.83[AMR][1000 genomes]
rs2659906	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659909	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659912	0.82[EUR][1000 genomes]
rs2659915	0.81[EUR][1000 genomes]
rs2659916	0.81[EUR][1000 genomes]
rs2707822	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707827	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2707836	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707841	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707845	0.83[AMR][1000 genomes]
rs2707849	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707850	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707852	0.83[AMR][1000 genomes]
rs2707853	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707854	0.80[AMR][1000 genomes]
rs2707856	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3069894	0.84[AMR][1000 genomes]
rs3800812	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3800823	0.80[EUR][1000 genomes]
rs3857688	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279493	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4717310	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62466793	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62466794	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6958520	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6979488	0.80[EUR][1000 genomes]
rs7779971	0.82[EUR][1000 genomes]
rs7782320	0.82[AMR][1000 genomes]
rs7783924	0.83[AMR][1000 genomes]
rs7785213	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7788576	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7789184	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7793569	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9791890	0.81[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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs28887326	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs28887326	RP4-756H11.3	cis	Thyroid	GTEx
rs28887326	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs28887326	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs28887326	RP4-756H11.3	cis	Artery Aorta	GTEx
rs28887326	RP4-756H11.3	cis	Artery Tibial	GTEx
rs28887326	RP4-756H11.3	cis	lung	GTEx
rs28887326	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs28887326	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28887326	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs28887326	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66148000-66177600	Weak transcription	Aorta	Aorta
2	chr7:66148200-66175600	Weak transcription	Primary B cells from cord blood	blood
3	chr7:66148400-66178400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:66148400-66182400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:66148400-66184400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:66148400-66184800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:66148600-66172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:66148600-66177400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:66149000-66177600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
11	chr7:66149600-66178400	Weak transcription	GM12878-XiMat	blood
12	chr7:66149600-66190200	Weak transcription	Hela-S3	cervix
13	chr7:66151400-66178400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:66153400-66178400	Weak transcription	Fetal Kidney	kidney
15	chr7:66153400-66182200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:66153600-66172200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:66153600-66174200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:66154000-66172600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:66154200-66172400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:66154200-66177400	Weak transcription	Fetal Intestine Large	intestine
21	chr7:66155200-66178400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:66158000-66177200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:66159000-66180000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:66159200-66175400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:66159400-66180000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:66159600-66172600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:66159600-66178000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:66159600-66178400	Weak transcription	Primary T cells from cord blood	blood
29	chr7:66159600-66190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:66159800-66177800	Weak transcription	HSMMtube	muscle
31	chr7:66159800-66180800	Weak transcription	Brain Germinal Matrix	brain
32	chr7:66160000-66177400	Weak transcription	Liver	Liver
33	chr7:66160200-66172600	Weak transcription	Fetal Lung	lung
34	chr7:66160600-66172400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:66162200-66172600	Weak transcription	Fetal Brain Female	brain
36	chr7:66162200-66177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:66162400-66177600	Weak transcription	Placenta	Placenta
38	chr7:66162400-66189400	Weak transcription	Psoas Muscle	Psoas
39	chr7:66162600-66172800	Weak transcription	Brain Substantia Nigra	brain
40	chr7:66162600-66174200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:66162600-66175800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:66162600-66177400	Weak transcription	NHLF	lung
43	chr7:66162600-66178400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:66162600-66178400	Weak transcription	NHEK	skin
45	chr7:66162600-66180600	Weak transcription	HMEC	breast
46	chr7:66162600-66192400	Weak transcription	NH-A	brain
47	chr7:66162600-66196800	Weak transcription	Right Ventricle	heart
48	chr7:66162800-66172400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:66162800-66177600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr7:66163000-66175000	Weak transcription	HSMM	muscle

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