Variant report

Variant	rs1966602
Chromosome Location	chr7:150829458-150829459
allele	A/G
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	chr7:150828372-150830723	K562	blood:	n/a	n/a
2	POLR2A	chr7:150828892-150829622	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:150825773..150828116-chr7:150828450..150830574,2	MCF-7	breast:
2	chr7:150817194..150819802-chr7:150827702..150830037,3	MCF-7	breast:
3	chr7:150822703..150826182-chr7:150829371..150831194,4	MCF-7	breast:
4	chr7:150812170..150814397-chr7:150827943..150830843,2	MCF-7	breast:

Variant related genes	Relation type
AGAP3	TF binding region
ENSG00000133612	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10952303	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4725393	0.81[EUR][1000 genomes]
rs6943608	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv539198	chr7:150643928-150879259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
4	nsv889477	chr7:150731698-150837529	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
5	nsv889478	chr7:150732812-150889527	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
6	nsv831188	chr7:150735204-150912875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv609013	chr7:150751590-150832913	Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv889481	chr7:150766799-150837529	Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
9	nsv889482	chr7:150766799-150851566	Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv889486	chr7:150775306-150891641	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
11	nsv523930	chr7:150822192-150830015	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv528732	chr7:150822192-150832913	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1966602	TMEM176A	cis	lymphoblastoid	seeQTL
rs1966602	ATP6V0E2	cis	parietal	SCAN
rs1966602	TMEM176B	cis	cerebellum	SCAN
rs1966602	TMEM176A	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150812400-150829600	Weak transcription	Small Intestine	intestine
2	chr7:150812600-150839800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:150813000-150840400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:150813000-150843800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:150814000-150842600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:150814200-150839800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:150814800-150839800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:150815600-150833600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:150815600-150843400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:150816200-150844000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr7:150820400-150842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:150821600-150833600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:150822800-150829600	Weak transcription	Primary T cells from cord blood	blood
14	chr7:150823200-150839600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:150823400-150831400	Weak transcription	Right Atrium	heart
16	chr7:150823400-150841800	Strong transcription	Lung	lung
17	chr7:150823600-150832600	Strong transcription	Spleen	Spleen
18	chr7:150823600-150841400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr7:150823600-150842400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:150823800-150832600	Weak transcription	Fetal Brain Male	brain
21	chr7:150823800-150835400	Strong transcription	NHLF	lung
22	chr7:150823800-150839800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:150823800-150842800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:150824000-150830800	Weak transcription	Left Ventricle	heart
25	chr7:150824000-150831200	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr7:150824000-150834000	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr7:150824000-150834200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:150824000-150834800	Strong transcription	NHEK	skin
29	chr7:150824000-150839000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:150824000-150842600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:150824000-150842600	Strong transcription	Liver	Liver
32	chr7:150824000-150843600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:150824200-150842800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:150824400-150829800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:150824400-150833600	Strong transcription	Gastric	stomach
36	chr7:150824400-150839200	Strong transcription	Adipose Nuclei	Adipose
37	chr7:150824600-150833800	Strong transcription	K562	blood
38	chr7:150824600-150834200	Strong transcription	HepG2	liver
39	chr7:150824600-150834400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:150824600-150834400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:150824600-150835000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:150824600-150835000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:150824600-150835600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr7:150824600-150835800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:150824600-150839400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:150824600-150841800	Strong transcription	Esophagus	oesophagus
47	chr7:150824800-150833800	Strong transcription	Fetal Brain Female	brain
48	chr7:150824800-150834000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr7:150824800-150842400	Strong transcription	Ovary	ovary
50	chr7:150825000-150830000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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