Variant report

Variant	rs7219624
Chromosome Location	chr17:59460164-59460165
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	EP300	chr17:59459910-59464367	SK-N-SH	brain:	n/a	chr17:59463203-59463217 chr17:59461941-59461954
2	TEAD4	chr17:59460065-59460859	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
2	chr17:59458290..59460742-chr3:12586329..12588287,2	MCF-7	breast:
3	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBX2-3	chr17:59460146-59460757	ENSG00000266934.1

Variant related genes	Relation type
ENSG00000266934	TF binding region
ENSG00000124243	Chromatin interaction
ENSG00000225526	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1004492	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs11079427	1.00[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3785839	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3785841	0.92[YRI][hapmap]
rs3785842	0.92[YRI][hapmap]
rs3785843	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3785844	0.90[CHB][hapmap]
rs4968557	1.00[CEU][hapmap]
rs7214149	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7216762	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8080537	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs929471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9891004	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9907356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9914215	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[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	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7219624	CHAD	trans	brain	seeQTL
rs7219624	MTNR1A	trans	brain	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59438200-59470800	Weak transcription	Esophagus	oesophagus
2	chr17:59440200-59462800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:59441600-59462200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:59444200-59460400	Weak transcription	Left Ventricle	heart
5	chr17:59444400-59467000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:59444600-59460600	Weak transcription	Right Ventricle	heart
7	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
8	chr17:59445000-59462200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr17:59446800-59464600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
11	chr17:59447200-59467000	Weak transcription	Gastric	stomach
12	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
13	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:59454600-59462600	Enhancers	NHDF-Ad	bronchial
15	chr17:59455200-59463400	Weak transcription	HSMMtube	muscle
16	chr17:59455600-59466800	Weak transcription	Lung	lung
17	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
18	chr17:59456600-59461800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:59456800-59460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:59456800-59464800	Weak transcription	Primary T cells from cord blood	blood
21	chr17:59457000-59461400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr17:59457200-59461200	Weak transcription	Spleen	Spleen
23	chr17:59457400-59460400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:59457400-59460600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr17:59457800-59461000	Enhancers	HepG2	liver
26	chr17:59457800-59463000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:59458000-59467000	Weak transcription	Osteobl	bone
28	chr17:59458200-59460400	Weak transcription	Adipose Nuclei	Adipose
29	chr17:59458200-59461600	Weak transcription	Placenta	Placenta
30	chr17:59458600-59467200	Weak transcription	Fetal Kidney	kidney
31	chr17:59458800-59466600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:59459000-59461400	Enhancers	Fetal Muscle Trunk	muscle
33	chr17:59459200-59460200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:59459200-59460200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:59459200-59460200	Weak transcription	Fetal Lung	lung
36	chr17:59459200-59460600	Weak transcription	NHLF	lung
37	chr17:59459200-59461200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr17:59459200-59462000	Weak transcription	Fetal Brain Female	brain
39	chr17:59459200-59463200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:59459200-59466800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr17:59459200-59469400	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:59459400-59463400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:59460000-59463800	Enhancers	Fetal Muscle Leg	muscle
44	chr17:59460000-59464000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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