Variant report

Variant	rs755690
Chromosome Location	chr19:39167360-39167361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39165775..39169288-chr19:39170285..39176842,12	K562	blood:
2	chr19:39147217..39149377-chr19:39166896..39169670,2	K562	blood:
3	chr19:39033486..39035242-chr19:39166999..39169094,2	K562	blood:
4	chr19:39127191..39129568-chr19:39165594..39168572,2	K562	blood:
5	chr19:39165622..39167893-chr19:39189221..39191148,2	K562	blood:
6	chr19:39166875..39169119-chr19:39190078..39191942,2	MCF-7	breast:
7	chr19:39166293..39168892-chr19:39172787..39174443,3	MCF-7	breast:
8	chr19:39164276..39166665-chr19:39166865..39169150,2	K562	blood:

No data

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1031849	0.84[ASN][1000 genomes]
rs10421863	0.84[CHD][hapmap]
rs10424568	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10426809	0.92[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1060186	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11083473	0.82[EUR][1000 genomes]
rs11665964	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11670636	0.85[AMR][1000 genomes]
rs12462503	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12984247	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1564203	0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1985636	0.85[ASN][1000 genomes]
rs2080988	0.92[ASN][1000 genomes]
rs2112649	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2112651	0.83[ASN][1000 genomes]
rs3786841	0.91[ASN][1000 genomes]
rs3786843	0.94[ASN][1000 genomes]
rs4347742	0.92[ASN][1000 genomes]
rs4801861	0.90[CHD][hapmap];0.87[JPT][hapmap]
rs4802743	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6508813	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6508814	0.87[ASN][1000 genomes]
rs7252630	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs749701	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs752067	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8099948	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8107877	1.00[JPT][hapmap]
rs888996	0.83[ASN][1000 genomes]
rs888997	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9304576	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs9304577	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs936524	0.92[CHD][hapmap];1.00[JPT][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	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs755690	MEGF8	cis	cerebellum	SCAN
rs755690	ZNF223	cis	cerebellum	SCAN
rs755690	ZNF526	cis	cerebellum	SCAN
rs755690	EXOSC5	cis	parietal	SCAN
rs755690	PSG3	cis	parietal	SCAN
rs755690	LGALS17A	cis	cerebellum	SCAN
rs755690	PSMC4	cis	cerebellum	SCAN
rs755690	ERCC1	cis	cerebellum	SCAN
rs755690	ZNF180	cis	cerebellum	SCAN
rs755690	RPS16	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39158800-39167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:39159600-39169600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
4	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
5	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
6	chr19:39162200-39173400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:39162400-39172000	Enhancers	Left Ventricle	heart
8	chr19:39162600-39169400	Genic enhancers	A549	lung
9	chr19:39162800-39169400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:39162800-39173200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:39163800-39167600	Enhancers	Placenta	Placenta
12	chr19:39164400-39167600	Enhancers	Adipose Nuclei	Adipose
13	chr19:39164400-39172600	Enhancers	Small Intestine	intestine
14	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
15	chr19:39164600-39167400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr19:39164600-39167400	Enhancers	Lung	lung
17	chr19:39164600-39167600	Enhancers	Brain Substantia Nigra	brain
18	chr19:39164600-39167600	Enhancers	Right Ventricle	heart
19	chr19:39164600-39167800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr19:39164600-39167800	Enhancers	Fetal Lung	lung
21	chr19:39164600-39168000	Genic enhancers	Fetal Stomach	stomach
22	chr19:39164600-39170400	Enhancers	Right Atrium	heart
23	chr19:39164600-39170800	Genic enhancers	Osteobl	bone
24	chr19:39164600-39173800	Genic enhancers	HepG2	liver
25	chr19:39164600-39178200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr19:39164800-39167400	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr19:39164800-39167400	Enhancers	NHLF	lung
28	chr19:39164800-39167600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr19:39164800-39167600	Enhancers	Esophagus	oesophagus
30	chr19:39164800-39167600	Flanking Active TSS	K562	blood
31	chr19:39164800-39167800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:39164800-39167800	Enhancers	Brain Anterior Caudate	brain
33	chr19:39164800-39167800	Enhancers	Brain Cingulate Gyrus	brain
34	chr19:39164800-39167800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr19:39164800-39167800	Genic enhancers	HSMM	muscle
36	chr19:39164800-39168400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:39164800-39169800	Enhancers	Primary hematopoietic stem cells	blood
38	chr19:39164800-39170200	Genic enhancers	Rectal Mucosa Donor 29	rectum
39	chr19:39164800-39170600	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:39164800-39170800	Enhancers	Brain Hippocampus Middle	brain
41	chr19:39164800-39170800	Enhancers	Psoas Muscle	Psoas
42	chr19:39164800-39171000	Genic enhancers	Rectal Mucosa Donor 31	rectum
43	chr19:39164800-39171400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:39164800-39172600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr19:39164800-39173800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:39164800-39177600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr19:39164800-39179200	Enhancers	Pancreas	Pancrea
48	chr19:39164800-39179800	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr19:39165000-39167400	Enhancers	Gastric	stomach

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