Variant report

Variant	rs12609635
Chromosome Location	chr19:44660967-44660968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44659490..44662168-chr19:44665073..44667043,2	MCF-7	breast:
2	chr19:44658613..44663687-chr19:44664925..44670649,9	K562	blood:

Variant related genes	Relation type
ENSG00000167380	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10409155	0.90[ASN][1000 genomes]
rs10417451	0.88[ASN][1000 genomes]
rs1107064	0.86[JPT][hapmap]
rs11666199	0.92[ASN][1000 genomes]
rs11667521	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11671074	0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap]
rs12459795	0.99[ASN][1000 genomes]
rs12460431	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12461251	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12462557	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs12462723	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs12972784	0.94[ASN][1000 genomes]
rs2051058	0.89[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2051059	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2125579	0.82[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2356727	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2356752	0.94[ASN][1000 genomes]
rs4592768	0.85[AFR][1000 genomes]
rs4802209	0.88[ASN][1000 genomes]
rs4802210	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4802217	0.80[AFR][1000 genomes]
rs4802218	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs4803684	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs62117771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509145	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7248054	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7253196	0.94[ASN][1000 genomes]
rs7508523	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8103838	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8105073	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs8105479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8108934	0.97[ASN][1000 genomes]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12609635	HRC	cis	parietal	SCAN
rs12609635	APOC4	cis	parietal	SCAN
rs12609635	ZNF350	cis	parietal	SCAN
rs12609635	BCAT2	cis	cerebellum	SCAN
rs12609635	ZNF175	cis	cerebellum	SCAN
rs12609635	SYMPK	cis	cerebellum	SCAN
rs12609635	GNG8	cis	parietal	SCAN
rs12609635	ZNF766	cis	parietal	SCAN
rs12609635	KLK10	cis	parietal	SCAN
rs12609635	SIGLEC16	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44647800-44668400	ZNF genes & repeats	Liver	Liver
2	chr19:44648400-44663200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:44648600-44661800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr19:44648800-44661200	Strong transcription	Fetal Intestine Large	intestine
5	chr19:44652200-44662200	ZNF genes & repeats	Ovary	ovary
6	chr19:44652200-44662800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:44652400-44667600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr19:44652800-44661400	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr19:44652800-44662400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:44653800-44668200	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr19:44654200-44662000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:44654600-44662200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
13	chr19:44654600-44662400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:44654600-44662400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:44655800-44662400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
16	chr19:44656000-44662200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
17	chr19:44656200-44662000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr19:44656200-44662400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr19:44656200-44662400	ZNF genes & repeats	Fetal Lung	lung
20	chr19:44656200-44662600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr19:44656400-44662600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:44657400-44662200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
23	chr19:44657600-44662000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
24	chr19:44657600-44663600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:44657800-44662400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr19:44657800-44663200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr19:44657800-44663200	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr19:44658000-44662000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
29	chr19:44658000-44662200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:44658000-44662200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
31	chr19:44658000-44662400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:44658000-44662600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr19:44658200-44661600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:44658200-44661600	Strong transcription	Fetal Stomach	stomach
35	chr19:44658200-44661800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr19:44658200-44662200	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr19:44658200-44662400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:44658200-44662600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
39	chr19:44658200-44662800	ZNF genes & repeats	Aorta	Aorta
40	chr19:44658600-44662200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
41	chr19:44658800-44661600	Strong transcription	HepG2	liver
42	chr19:44658800-44662200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:44658800-44662200	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr19:44658800-44662400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:44659000-44662200	ZNF genes & repeats	Dnd41	blood
46	chr19:44659000-44662400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr19:44659000-44662600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:44659400-44662200	ZNF genes & repeats	Fetal Kidney	kidney
49	chr19:44659400-44662200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:44659400-44662200	ZNF genes & repeats	NHEK	skin

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