Variant report

Variant	rs219229
Chromosome Location	chr7:150940867-150940868
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	SMC3	chr7:150940796-150943624	SK-N-SH	brain:	n/a	chr7:150941980-150941987 chr7:150941567-150941581 chr7:150941940-150941947
2	POLR2A	chr7:150940730-150940993	MCF-7	breast:	n/a	n/a
3	CTCF	chr7:150940291-150943350	SK-N-SH	brain:	n/a	chr7:150941938-150941951 chr7:150940479-150940497 chr7:150941560-150941581 chr7:150941941-150941954 chr7:150940585-150940598 chr7:150941920-150941929 chr7:150941977-150941986
4	POLR2A	chr7:150940719-150941426	U87	brain:	n/a	n/a
5	POLR2A	chr7:150935782-150941408	U87	brain:	n/a	n/a
6	IRF1	chr7:150940419-150940893	K562	blood:	n/a	chr7:150940637-150940651 chr7:150940637-150940647 chr7:150940636-150940648 chr7:150940635-150940648 chr7:150940637-150940648 chr7:150940635-150940649 chr7:150940631-150940652 chr7:150940633-150940647 chr7:150940638-150940649
7	YY1	chr7:150940690-150940933	GM12891	blood:	n/a	n/a
8	ZNF384	chr7:150940799-150940953	K562	blood:	n/a	chr7:150940804-150940812
9	POLR2A	chr7:150932457-150941238	U87	brain:	n/a	n/a
10	POLR2A	chr7:150940732-150940914	K562	blood:	n/a	n/a
11	POLR2A	chr7:150940769-150941426	U87	brain:	n/a	n/a
12	RCOR1	chr7:150940862-150940938	K562	blood:	n/a	n/a
13	RAD21	chr7:150940770-150943041	SK-N-SH	brain:	n/a	chr7:150941937-150941950 chr7:150941591-150941603 chr7:150941563-150941582 chr7:150941940-150941954

No.	Distal block	Cell Line	Cell type
1	chr7:150923495..150927436-chr7:150940006..150942925,4	MCF-7	breast:
2	chr7:150938571..150942838-chr7:150950941..150954111,4	MCF-7	breast:
3	chr7:150819780..150822617-chr7:150940406..150943194,3	MCF-7	breast:

Variant related genes	Relation type
SMARCD3	TF binding region
ENSG00000033050	Chromatin interaction
ENSG00000133612	Chromatin interaction
ENSG00000082014	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12538502	0.83[ASN][1000 genomes]
rs2045465	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs219230	0.85[ASN][1000 genomes]
rs219233	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]
rs2252694	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2487157	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2608289	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[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];0.90[ASN][1000 genomes]
rs2792431	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2792433	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807387	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236429	0.81[AFR][1000 genomes]
rs4236430	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs4726007	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6464133	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6958591	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs7786030	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs219229	GIMAP8	cis	parietal	SCAN
rs219229	ABCF2	cis	Thyroid	GTEx

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

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	chr7:150932800-150942000	Weak transcription	Psoas Muscle	Psoas
4	chr7:150936400-150941200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:150936400-150942200	Weak transcription	HMEC	breast
6	chr7:150936800-150941000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:150936800-150941800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:150937400-150941200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:150937600-150941200	Weak transcription	Right Atrium	heart
10	chr7:150938600-150941800	Weak transcription	NH-A	brain
11	chr7:150938800-150941000	Weak transcription	Fetal Heart	heart
12	chr7:150939200-150941600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:150939200-150941600	Weak transcription	A549	lung
14	chr7:150939200-150942000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:150939200-150942000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:150939400-150941000	Weak transcription	Gastric	stomach
17	chr7:150939400-150941800	Enhancers	Fetal Brain Male	brain
18	chr7:150939400-150941800	Enhancers	HepG2	liver
19	chr7:150939600-150941800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:150939600-150941800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr7:150939600-150942000	Weak transcription	Aorta	Aorta
22	chr7:150939800-150941200	Weak transcription	Ovary	ovary
23	chr7:150939800-150941400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:150939800-150941600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:150939800-150941600	Genic enhancers	Fetal Muscle Leg	muscle
26	chr7:150939800-150941600	Weak transcription	Osteobl	bone
27	chr7:150939800-150941800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr7:150940000-150941000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:150940000-150941000	Genic enhancers	Right Ventricle	heart
30	chr7:150940000-150941000	Weak transcription	HSMMtube	muscle
31	chr7:150940000-150941200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:150940000-150941200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr7:150940000-150941200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr7:150940000-150941200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr7:150940000-150941400	Flanking Active TSS	Dnd41	blood
36	chr7:150940000-150941800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:150940000-150941800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:150940000-150942200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:150940000-150942200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr7:150940000-150942400	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr7:150940000-150942800	Enhancers	Spleen	Spleen
42	chr7:150940200-150941000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:150940200-150941000	Weak transcription	Fetal Lung	lung
44	chr7:150940200-150941200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr7:150940200-150941200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:150940200-150941400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:150940200-150941400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr7:150940200-150941400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:150940200-150941400	Genic enhancers	NHLF	lung
50	chr7:150940200-150941600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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