Variant report

Variant	rs6509146
Chromosome Location	chr19:44646572-44646573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44644669..44647100-chr19:44951741..44953337,2	K562	blood:
2	chr19:44616455..44619109-chr19:44645010..44647245,2	K562	blood:
3	chr19:44596713..44600957-chr19:44644435..44647275,5	MCF-7	breast:
4	chr19:44643597..44647343-chr19:44667648..44671629,7	K562	blood:
5	chr19:44646506..44648023-chr19:44661146..44663023,2	K562	blood:
6	chr19:44616201..44619073-chr19:44644939..44647380,2	MCF-7	breast:
7	chr19:44644162..44647190-chr19:44667490..44670508,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186019	Chromatin interaction
ENSG00000256294	Chromatin interaction
ENSG00000267188	Chromatin interaction
ENSG00000167383	Chromatin interaction
ENSG00000267680	Chromatin interaction
ENSG00000167380	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10405450	0.86[ASN][1000 genomes]
rs10409155	0.90[EUR][1000 genomes]
rs10410086	0.86[ASN][1000 genomes]
rs10425945	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11667521	0.83[GIH][hapmap]
rs12460039	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12462557	0.85[GIH][hapmap]
rs12462723	0.85[GIH][hapmap]
rs12608984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2100643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168989	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2232801	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2279072	0.83[GIH][hapmap]
rs2279073	0.83[GIH][hapmap]
rs2293587	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356752	0.88[EUR][1000 genomes]
rs3817595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802209	0.90[EUR][1000 genomes]
rs4802210	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4803684	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs56357907	0.89[ASN][1000 genomes]
rs58778698	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60668498	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61412562	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61589395	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62117770	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7248114	0.87[ASN][1000 genomes]
rs7249209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251682	0.81[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7253533	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7260304	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs8103838	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs9304640	0.90[JPT][hapmap]
rs9646643	0.82[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6509146	SIGLEC9	cis	parietal	SCAN
rs6509146	DHDH	cis	parietal	SCAN
rs6509146	APOC1	cis	parietal	SCAN
rs6509146	ZNF575	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44644200-44646600	Active TSS	Colon Smooth Muscle	Colon
2	chr19:44644800-44646600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr19:44644800-44646600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:44644800-44646600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr19:44644800-44646600	Active TSS	Psoas Muscle	Psoas
6	chr19:44644800-44646800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:44644800-44646800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:44644800-44646800	Active TSS	Fetal Intestine Small	intestine
9	chr19:44644800-44647000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:44644800-44647000	Active TSS	HSMMtube	muscle
11	chr19:44644800-44647400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:44645000-44646600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:44645000-44646600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:44645000-44646600	Active TSS	Esophagus	oesophagus
15	chr19:44645000-44646600	Active TSS	Hela-S3	cervix
16	chr19:44645000-44646600	Bivalent/Poised TSS	HepG2	liver
17	chr19:44645000-44646800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:44645000-44646800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:44645000-44646800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:44645000-44646800	Active TSS	Colonic Mucosa	Colon
21	chr19:44645000-44646800	Active TSS	Fetal Muscle Trunk	muscle
22	chr19:44645000-44646800	Active TSS	Ovary	ovary
23	chr19:44645000-44647000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:44645000-44647000	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr19:44645000-44647000	Active TSS	NHDF-Ad	bronchial
26	chr19:44645200-44646600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr19:44645200-44646600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:44645200-44646600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:44645200-44646600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:44645200-44646600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:44645200-44646600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:44645200-44646600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:44645200-44646600	Active TSS	Fetal Intestine Large	intestine
34	chr19:44645200-44646600	Active TSS	Fetal Stomach	stomach
35	chr19:44645200-44646600	Active TSS	Pancreas	Pancrea
36	chr19:44645200-44646600	Active TSS	Placenta Amnion	Placenta Amnion
37	chr19:44645200-44646600	Active TSS	Right Atrium	heart
38	chr19:44645200-44646800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr19:44645200-44646800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:44645200-44646800	Active TSS	Aorta	Aorta
41	chr19:44645200-44646800	Active TSS	Left Ventricle	heart
42	chr19:44645200-44646800	Active TSS	Lung	lung
43	chr19:44645200-44646800	Active TSS	HSMM	muscle
44	chr19:44645200-44647000	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr19:44645200-44647000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr19:44645200-44647000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:44645200-44647000	Active TSS	A549	lung
48	chr19:44645200-44647000	Active TSS	NHLF	lung
49	chr19:44645400-44646600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:44645400-44646600	Active TSS	Fetal Muscle Leg	muscle

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