Variant report

Variant	rs767540
Chromosome Location	chr19:44090509-44090510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44084551..44087114-chr19:44089060..44090571,2	MCF-7	breast:
2	chr19:44088845..44091778-chr19:44114568..44117428,2	K562	blood:
3	chr19:44088599..44091179-chr19:44091535..44093302,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XRCC1-2	chr19:44090088-44093839	NONHSAT066605

Variant related genes	Relation type
ENSG00000234465	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11083711	1.00[LWK][hapmap]
rs11671645	0.82[EUR][1000 genomes]
rs12461175	1.00[CEU][hapmap]
rs1402325	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs1402326	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17655484	0.90[JPT][hapmap]
rs17655574	1.00[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1879387	0.87[EUR][1000 genomes]
rs2003098	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2023614	0.90[JPT][hapmap];0.87[AFR][1000 genomes]
rs2079646	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs2302421	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes]
rs3213266	0.90[JPT][hapmap]
rs3213328	0.90[JPT][hapmap]
rs3746002	0.85[CEU][hapmap];0.84[GIH][hapmap];0.82[EUR][1000 genomes]
rs3746003	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs3815422	0.82[EUR][1000 genomes]
rs4803643	0.81[EUR][1000 genomes]
rs4803644	0.82[EUR][1000 genomes]
rs880108	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs939461	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs767540	PRRG2	cis	cerebellum	SCAN
rs767540	ZNF615	cis	cerebellum	SCAN
rs767540	IZUMO2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
2	chr19:44080600-44090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:44080600-44095600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:44081600-44090600	Weak transcription	HMEC	breast
5	chr19:44084600-44093000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:44084600-44093000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:44084600-44093000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:44084600-44093000	Weak transcription	HUVEC	blood vessel
9	chr19:44084600-44093800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:44084600-44094000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr19:44084600-44096800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:44084600-44098200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:44084800-44095400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr19:44084800-44097400	Weak transcription	NH-A	brain
15	chr19:44085000-44095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:44085000-44095600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:44085400-44094600	Weak transcription	Left Ventricle	heart
18	chr19:44085600-44090600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:44085600-44090600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:44085600-44094200	Weak transcription	Right Ventricle	heart
21	chr19:44085600-44095200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:44085600-44096200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:44085600-44096200	Weak transcription	Aorta	Aorta
24	chr19:44085600-44098800	Weak transcription	Psoas Muscle	Psoas
25	chr19:44085600-44099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:44085800-44093000	Weak transcription	NHLF	lung
27	chr19:44085800-44094200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:44085800-44094200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:44085800-44094600	Weak transcription	Esophagus	oesophagus
30	chr19:44085800-44094600	Weak transcription	Gastric	stomach
31	chr19:44085800-44095400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:44085800-44096200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:44085800-44096200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:44085800-44096600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:44086000-44090600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:44086000-44092800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:44086000-44093000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:44086000-44093000	Weak transcription	Brain Angular Gyrus	brain
39	chr19:44086000-44093000	Weak transcription	Brain Anterior Caudate	brain
40	chr19:44086000-44093200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:44086000-44093200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:44086000-44093200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr19:44086000-44093800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr19:44086000-44094200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr19:44086000-44094600	Weak transcription	Colon Smooth Muscle	Colon
46	chr19:44086000-44094800	Weak transcription	Brain Substantia Nigra	brain
47	chr19:44086000-44095200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:44086000-44098000	Weak transcription	NHDF-Ad	bronchial
49	chr19:44086200-44090800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:44086200-44094000	Weak transcription	Colonic Mucosa	Colon

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