Variant report

Variant	rs1870238
Chromosome Location	chr7:150936052-150936053
allele	C/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	chr7:150936047-150937056	HL-60	blood:	n/a	n/a
2	POLR2A	chr7:150935817-150936736	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:150935980-150936441	K562	blood:	n/a	n/a
4	POLR2A	chr7:150935927-150936962	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:150935363-150940669	U87	brain:	n/a	n/a
6	POLR2A	chr7:150935910-150936936	GM12892	blood:	n/a	n/a
7	POLR2A	chr7:150933683-150937991	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:150936021-150936193	HepG2	liver:	n/a	n/a
9	POLR2A	chr7:150935951-150937045	GM12891	blood:	n/a	n/a
10	SPI1	chr7:150936024-150936548	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:150935782-150941408	U87	brain:	n/a	n/a
12	POLR2A	chr7:150935878-150936940	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:150935975-150936911	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:150935911-150936176	K562	blood:	n/a	n/a
15	POLR2A	chr7:150936025-150936887	GM12892	blood:	n/a	n/a
16	POLR2A	chr7:150932336-150940594	K562	blood:	n/a	n/a
17	POLR2A	chr7:150936043-150936815	GM12892	blood:	n/a	n/a
18	POLR2A	chr7:150932457-150941238	U87	brain:	n/a	n/a
19	MTA3	chr7:150936029-150936445	GM12878	blood:	n/a	n/a
20	SPI1	chr7:150936039-150936368	GM12891	blood:	n/a	n/a
21	POLR2A	chr7:150935929-150938146	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:150936014-150937007	GM12891	blood:	n/a	n/a
23	POLR2A	chr7:150935942-150937591	K562	blood:	n/a	n/a
24	POLR2A	chr7:150935932-150940768	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000272661	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2242141	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256864	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2429248	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2446065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487152	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2487154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2487155	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2608288	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2608291	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2608292	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608293	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2792434	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2792435	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2792436	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800792	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3800793	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4725398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4726009	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4726010	0.91[ASN][1000 genomes]
rs6464134	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6949587	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs758249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs897917	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs921987	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	nsv609035	chr7:150896223-150955765	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv889487	chr7:150922952-150988172	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv889488	chr7:150926775-150955765	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1870238	ABCF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150930600-150940000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:150931000-150944600	Weak transcription	Fetal Kidney	kidney
3	chr7:150931200-150936200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
4	chr7:150931200-150936400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:150931200-150937400	Weak transcription	Right Atrium	heart
6	chr7:150931200-150938200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:150931200-150940000	Strong transcription	Fetal Intestine Small	intestine
8	chr7:150931200-150940000	Weak transcription	Stomach Mucosa	stomach
9	chr7:150931200-150940200	Strong transcription	Fetal Stomach	stomach
10	chr7:150931400-150936600	Weak transcription	Fetal Heart	heart
11	chr7:150931400-150936800	Strong transcription	A549	lung
12	chr7:150931400-150937400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:150931400-150937400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:150931400-150939000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:150931400-150939600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:150931400-150939800	Strong transcription	Lung	lung
17	chr7:150931400-150940200	Weak transcription	Small Intestine	intestine
18	chr7:150931400-150940200	Strong transcription	NHLF	lung
19	chr7:150931600-150937200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:150931600-150937400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:150931600-150937800	Strong transcription	Thymus	Thymus
22	chr7:150931600-150939200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:150931600-150939200	Strong transcription	Brain Hippocampus Middle	brain
24	chr7:150931600-150939200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:150931600-150939600	Strong transcription	Placenta	Placenta
26	chr7:150931600-150939800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr7:150931600-150939800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:150931600-150940000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:150931600-150940200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:150931600-150940200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:150931600-150940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:150931600-150944400	Weak transcription	Hela-S3	cervix
33	chr7:150931800-150937000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:150931800-150937000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr7:150931800-150937400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:150931800-150938800	Strong transcription	Fetal Intestine Large	intestine
37	chr7:150931800-150938800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr7:150931800-150939600	Strong transcription	Fetal Brain Female	brain
39	chr7:150932000-150936400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr7:150932000-150936600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:150932000-150936800	Strong transcription	Liver	Liver
42	chr7:150932000-150936800	Strong transcription	Brain Substantia Nigra	brain
43	chr7:150932000-150938400	Strong transcription	Fetal Thymus	thymus
44	chr7:150932000-150938600	Strong transcription	NHDF-Ad	bronchial
45	chr7:150932000-150938800	Strong transcription	Brain Germinal Matrix	brain
46	chr7:150932000-150939000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr7:150932000-150939600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:150932000-150939800	Strong transcription	Ovary	ovary
49	chr7:150932000-150940000	Strong transcription	Brain Anterior Caudate	brain
50	chr7:150932200-150936200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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