Variant report

Variant	rs320887
Chromosome Location	chr19:37693438-37693439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37691618..37694234-chr19:37698005..37700381,2	MCF-7	breast:
2	chr19:37692673..37695241-chr19:37698158..37700620,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267360	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1234250	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1533736	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17707446	1.00[JPT][hapmap]
rs184408	0.82[ASN][1000 genomes]
rs320876	0.83[EUR][1000 genomes]
rs320881	0.81[CEU][hapmap];0.93[TSI][hapmap]
rs320888	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs502546	0.84[CEU][hapmap]
rs7257135	1.00[JPT][hapmap]
rs862234	0.92[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs320887	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs320887	SIPA1L3	cis	cerebellum	SCAN
rs320887	AC012309.5	cis	Esophagus Mucosa	GTEx
rs320887	PLEKHG2	cis	cerebellum	SCAN
rs320887	ZNF781	cis	Thyroid	GTEx
rs320887	CCDC97	cis	cerebellum	SCAN
rs320887	HIPK4	cis	parietal	SCAN
rs320887	PVR	cis	parietal	SCAN
rs320887	POU2F2	cis	parietal	SCAN
rs320887	AC012309.5	cis	Thyroid	GTEx
rs320887	AC012309.5	cis	Heart Left Ventricle	GTEx
rs320887	PAK4	cis	cerebellum	SCAN
rs320887	AC012309.5	cis	Artery Tibial	GTEx
rs320887	HKR1	cis	Whole Blood	GTEx
rs320887	ZNF585B	cis	Artery Tibial	GTEx
rs320887	ARHGEF1	cis	cerebellum	SCAN
rs320887	AC012309.5	cis	Esophagus Muscularis	GTEx
rs320887	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37675000-37701000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37679000-37700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:37680600-37700800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:37680800-37695000	Weak transcription	HSMM	muscle
5	chr19:37680800-37700800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:37680800-37700800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:37681000-37695800	Weak transcription	NH-A	brain
8	chr19:37681000-37695800	Weak transcription	NHLF	lung
9	chr19:37681000-37700800	Weak transcription	HSMMtube	muscle
10	chr19:37681000-37700800	Weak transcription	HUVEC	blood vessel
11	chr19:37681000-37701000	Weak transcription	Fetal Heart	heart
12	chr19:37681200-37696600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:37683200-37695200	Weak transcription	Brain Substantia Nigra	brain
14	chr19:37683400-37697400	Weak transcription	Fetal Brain Male	brain
15	chr19:37686800-37696600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:37686800-37699000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:37687000-37700800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:37687400-37696000	Weak transcription	NHEK	skin
19	chr19:37687600-37698400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:37688200-37695400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:37688600-37699000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37688800-37693800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:37688800-37698200	Strong transcription	Placenta	Placenta
24	chr19:37689000-37701000	Weak transcription	Stomach Mucosa	stomach
25	chr19:37689200-37695000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr19:37689200-37698400	ZNF genes & repeats	Liver	Liver
27	chr19:37689400-37700800	Weak transcription	Psoas Muscle	Psoas
28	chr19:37689800-37699800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:37690200-37695000	Weak transcription	Brain Anterior Caudate	brain
30	chr19:37690200-37695200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:37690200-37701000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:37690200-37701000	Weak transcription	Fetal Kidney	kidney
33	chr19:37690400-37693600	Weak transcription	Aorta	Aorta
34	chr19:37690400-37693800	Weak transcription	Primary T cells from cord blood	blood
35	chr19:37690400-37694400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr19:37690400-37695000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:37690400-37695000	Weak transcription	Gastric	stomach
38	chr19:37690400-37695200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:37690400-37695200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:37690400-37695200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:37690400-37695200	Weak transcription	Esophagus	oesophagus
42	chr19:37690400-37695200	Weak transcription	Thymus	Thymus
43	chr19:37690400-37695400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:37690400-37695600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:37690400-37696000	Weak transcription	NHDF-Ad	bronchial
46	chr19:37690400-37697600	Weak transcription	Brain Angular Gyrus	brain
47	chr19:37690400-37698200	Strong transcription	Adipose Nuclei	Adipose
48	chr19:37690400-37700600	Weak transcription	Right Ventricle	heart
49	chr19:37690400-37700800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr19:37690600-37693600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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