Variant report

Variant	rs2288651
Chromosome Location	chr7:150825492-150825493
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	chr7:150825462-150826009	K562	blood:	n/a	n/a
2	POLR2A	chr7:150825235-150828231	K562	blood:	n/a	n/a
3	POLR2A	chr7:150825385-150825700	K562	blood:	n/a	n/a
4	POLR2A	chr7:150825270-150826299	K562	blood:	n/a	n/a
5	POLR2A	chr7:150825433-150825540	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:150825335-150825729	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:150823153..150825845-chr7:150864127..150866768,5	MCF-7	breast:
2	chr7:150818782..150822666-chr7:150823705..150827002,4	MCF-7	breast:
3	chr7:150825310..150827714-chr7:151037547..151039688,2	K562	blood:

Variant related genes	Relation type
AGAP3	TF binding region
ENSG00000133612	Chromatin interaction
ENSG00000013374	Chromatin interaction
ENSG00000164900	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10230113	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2288652	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55816533	0.84[ASN][1000 genomes]
rs62489625	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62489626	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729711	0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7776766	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7777517	0.88[ASN][1000 genomes]
rs7808252	0.86[AFR][1000 genomes];0.88[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2288651	ATP6V0E2	cis	parietal	SCAN
rs2288651	GIMAP2	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	chr7:150814000-150828600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:150814000-150842600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:150814200-150839800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:150814800-150839800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:150815600-150833600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:150815600-150843400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:150816200-150844000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:150818400-150826600	Weak transcription	HSMMtube	muscle
13	chr7:150819400-150827600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr7:150820400-150842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:150821400-150825600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr7:150821600-150833600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:150822400-150825600	Weak transcription	Brain Angular Gyrus	brain
18	chr7:150822400-150825800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:150822400-150827200	Weak transcription	Dnd41	blood
20	chr7:150822600-150826000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:150822600-150827000	Weak transcription	HUVEC	blood vessel
22	chr7:150822600-150828000	Weak transcription	HSMM	muscle
23	chr7:150822800-150827000	Weak transcription	Fetal Kidney	kidney
24	chr7:150822800-150827200	Weak transcription	A549	lung
25	chr7:150822800-150827200	Weak transcription	GM12878-XiMat	blood
26	chr7:150822800-150829600	Weak transcription	Primary T cells from cord blood	blood
27	chr7:150823000-150825600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:150823000-150826600	Weak transcription	Hela-S3	cervix
29	chr7:150823000-150829000	Weak transcription	NHDF-Ad	bronchial
30	chr7:150823200-150839600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:150823400-150826600	Weak transcription	Aorta	Aorta
32	chr7:150823400-150827000	Weak transcription	NH-A	brain
33	chr7:150823400-150831400	Weak transcription	Right Atrium	heart
34	chr7:150823400-150841800	Strong transcription	Lung	lung
35	chr7:150823600-150825600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:150823600-150832600	Strong transcription	Spleen	Spleen
37	chr7:150823600-150841400	Genic enhancers	Fetal Muscle Leg	muscle
38	chr7:150823600-150842400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:150823800-150832600	Weak transcription	Fetal Brain Male	brain
40	chr7:150823800-150835400	Strong transcription	NHLF	lung
41	chr7:150823800-150839800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr7:150823800-150842800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:150824000-150827000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr7:150824000-150828400	Strong transcription	Placenta	Placenta
45	chr7:150824000-150828600	Weak transcription	Fetal Heart	heart
46	chr7:150824000-150830800	Weak transcription	Left Ventricle	heart
47	chr7:150824000-150831200	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr7:150824000-150834000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr7:150824000-150834200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr7:150824000-150834800	Strong transcription	NHEK	skin

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