Variant report

Variant	rs7607162
Chromosome Location	chr2:187378709-187378710
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:187378179..187380116-chr2:187380297..187381882,2	K562	blood:
2	chr2:187372828..187374469-chr2:187377188..187379476,2	K562	blood:
3	chr2:187374448..187380167-chr2:187454386..187459436,9	MCF-7	breast:
4	chr2:187378645..187382692-chr2:187454130..187456514,4	MCF-7	breast:
5	chr2:187369033..187372134-chr2:187377383..187380441,5	K562	blood:
6	chr2:187377349..187379042-chr2:187478698..187480439,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZC3H15-2	chr2:187378238-187379347	NONHSAT075998

No data

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction
ENSG00000065548	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10172850	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10192067	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10931245	0.81[ASN][1000 genomes]
rs11673938	0.81[ASN][1000 genomes]
rs1375326	0.82[ASN][1000 genomes]
rs1470230	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1975594	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2044919	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2119865	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2305409	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3768775	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3768776	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4144786	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4144822	0.81[ASN][1000 genomes]
rs4666704	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4666705	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4667093	0.80[ASN][1000 genomes]
rs4667094	0.80[ASN][1000 genomes]
rs4667097	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4667098	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4667099	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4667100	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4667101	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4667102	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6434181	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6717081	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6732188	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6732449	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6740632	0.81[ASN][1000 genomes]
rs6741184	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6747289	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6749314	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7556814	0.84[ASN][1000 genomes]
rs7562659	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7568700	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7569642	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7570883	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7582052	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7587410	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7595269	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs988110	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7607162	RP11-410E4.1	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187357000-187379000	Strong transcription	Fetal Thymus	thymus
2	chr2:187357400-187383000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:187357600-187382600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:187357600-187386200	Strong transcription	Dnd41	blood
5	chr2:187358200-187379000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:187358600-187379000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:187358600-187385800	Weak transcription	Esophagus	oesophagus
8	chr2:187359600-187386400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:187359800-187379000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:187359800-187379200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:187359800-187379400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:187359800-187379800	Strong transcription	HSMM	muscle
13	chr2:187359800-187380400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:187359800-187381400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:187359800-187387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:187360000-187378800	Strong transcription	Liver	Liver
17	chr2:187360000-187379200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:187360000-187386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:187360200-187379000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr2:187360200-187379200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:187360800-187379400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:187361200-187385600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:187361400-187389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:187363000-187385600	Weak transcription	Aorta	Aorta
25	chr2:187363000-187387800	Weak transcription	Pancreas	Pancrea
26	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:187363200-187397600	Weak transcription	Small Intestine	intestine
28	chr2:187364800-187379000	Strong transcription	Placenta	Placenta
29	chr2:187367200-187385600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:187367200-187396800	Weak transcription	Gastric	stomach
31	chr2:187367200-187405800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:187368600-187379000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:187368800-187378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:187369200-187383400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:187370800-187385600	Weak transcription	Fetal Stomach	stomach
36	chr2:187370800-187385600	Weak transcription	Spleen	Spleen
37	chr2:187370800-187385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:187370800-187385800	Weak transcription	Lung	lung
39	chr2:187370800-187386800	Weak transcription	Stomach Mucosa	stomach
40	chr2:187371000-187385800	Weak transcription	Thymus	Thymus
41	chr2:187371000-187389400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:187371000-187395800	Weak transcription	Fetal Heart	heart
43	chr2:187371000-187407800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:187371400-187385600	Weak transcription	Ovary	ovary
45	chr2:187372200-187390000	Weak transcription	Fetal Brain Male	brain
46	chr2:187373600-187385600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:187373600-187385600	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:187373600-187388000	Weak transcription	Psoas Muscle	Psoas
49	chr2:187373600-187395800	Weak transcription	HSMMtube	muscle
50	chr2:187373600-187397600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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