Variant report

Variant	rs219233
Chromosome Location	chr7:150944124-150944125
allele	G/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	chr7:150942456-150946649	IMR90	lung:	n/a	n/a
2	MAZ	chr7:150943987-150945269	IMR90	lung:	n/a	chr7:150944835-150944842 chr7:150944833-150944844 chr7:150944834-150944843
3	MXI1	chr7:150943671-150947189	IMR90	lung:	n/a	chr7:150944194-150944203 chr7:150945408-150945423
4	ZNF263	chr7:150942876-150947378	HEK293-T-REx	kidney:	n/a	chr7:150943567-150943576 chr7:150943679-150943688 chr7:150943760-150943769 chr7:150946929-150946938 chr7:150947019-150947028
5	MAX	chr7:150943912-150944511	K562	blood:	n/a	n/a
6	CTCF	chr7:150944020-150944170	GM12873	blood:	n/a	n/a
7	NR2F2	chr7:150943966-150944866	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150941406..150944514-chr7:150945051..150947075,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243018	TF binding region
SMARCD3	TF binding region
ENSG00000082014	Chromatin interaction
ENSG00000243018	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12538502	0.81[ASN][1000 genomes]
rs2045465	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs219229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs219230	0.82[ASN][1000 genomes]
rs2252694	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2487157	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2608289	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2608290	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2792431	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2792433	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789823	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs3807386	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807387	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4236429	0.81[AFR][1000 genomes]
rs4236430	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs4726007	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464133	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6958591	0.90[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs219233	ABCF2	cis	Thyroid	GTEx
rs219233	GIMAP8	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150931000-150944600	Weak transcription	Fetal Kidney	kidney
2	chr7:150931600-150944400	Weak transcription	Hela-S3	cervix
3	chr7:150940200-150944800	Enhancers	Pancreas	Pancrea
4	chr7:150940200-150945400	Enhancers	K562	blood
5	chr7:150940800-150944800	Bivalent Enhancer	Placenta	Placenta
6	chr7:150941200-150944800	Enhancers	NHDF-Ad	bronchial
7	chr7:150941600-150945600	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr7:150941800-150945600	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr7:150942000-150944800	Enhancers	Esophagus	oesophagus
10	chr7:150942000-150945200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr7:150942000-150945600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:150942200-150945000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:150942200-150945000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:150942400-150944800	Enhancers	Fetal Brain Male	brain
15	chr7:150942600-150944200	Enhancers	Brain Hippocampus Middle	brain
16	chr7:150942600-150944600	Enhancers	Brain Angular Gyrus	brain
17	chr7:150942800-150944600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr7:150942800-150945000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:150942800-150945200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr7:150942800-150945400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr7:150943000-150944200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr7:150943000-150944200	Enhancers	Brain Cingulate Gyrus	brain
23	chr7:150943000-150944400	Enhancers	Left Ventricle	heart
24	chr7:150943000-150944400	Enhancers	Psoas Muscle	Psoas
25	chr7:150943000-150944400	Flanking Active TSS	HSMM	muscle
26	chr7:150943000-150944800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr7:150943000-150944800	Enhancers	Brain Anterior Caudate	brain
28	chr7:150943000-150944800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr7:150943000-150945000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:150943000-150945000	Enhancers	Spleen	Spleen
31	chr7:150943000-150945200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr7:150943000-150945400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
33	chr7:150943200-150944200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr7:150943200-150944400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:150943200-150944400	Enhancers	NH-A	brain
36	chr7:150943200-150944600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:150943200-150944600	Bivalent Enhancer	Colonic Mucosa	Colon
38	chr7:150943200-150944600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
39	chr7:150943200-150944600	Enhancers	A549	lung
40	chr7:150943200-150944800	Weak transcription	HUVEC	blood vessel
41	chr7:150943200-150945000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:150943200-150945200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr7:150943200-150945400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
44	chr7:150943200-150945400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:150943400-150944400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:150943400-150944800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:150943400-150944800	Enhancers	Gastric	stomach
48	chr7:150943400-150945000	Flanking Active TSS	HSMMtube	muscle
49	chr7:150943400-150945200	Flanking Active TSS	Fetal Brain Female	brain
50	chr7:150943400-150945600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

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