Variant report

Variant	rs4802185
Chromosome Location	chr19:44026922-44026923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44019122-44027267	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44025500..44027391-chr19:44035173..44037345,2	MCF-7	breast:
2	chr19:44024381..44027679-chr19:44027727..44032202,4	MCF-7	breast:
3	chr19:44026787..44028868-chr19:44029356..44031374,2	K562	blood:

Variant related genes	Relation type
ZNF575	TF binding region
ENSG00000176472	Chromatin interaction
ENSG00000105755	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12460021	0.85[EUR][1000 genomes]
rs12973764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12979907	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12980646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12981023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs184239	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1978008	0.82[EUR][1000 genomes]
rs2102954	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682585	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2682586	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs2854501	0.91[ASW][hapmap];0.88[MEX][hapmap]
rs2854506	0.84[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs2854507	0.82[EUR][1000 genomes]
rs2854508	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2854509	0.84[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs304731	0.87[CEU][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs3213295	0.82[EUR][1000 genomes]
rs3213334	0.88[MEX][hapmap]
rs3213391	0.86[EUR][1000 genomes]
rs34977009	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35016410	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35485252	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36075334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810381	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4507015	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4544340	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59000923	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59827264	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61607741	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6509094	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71362654	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248167	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs7248927	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253856	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs762506	0.84[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs8100211	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4802185	ETHE1	cis	lymphoblastoid	seeQTL
rs4802185	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL
rs4802185	BLOC1S3	cis	parietal	SCAN
rs4802185	ETHE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44009200-44029200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:44009200-44029600	Weak transcription	Psoas Muscle	Psoas
3	chr19:44011200-44029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:44013000-44028600	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:44013000-44028800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:44013200-44028600	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
8	chr19:44013400-44029400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:44014400-44029400	Weak transcription	Dnd41	blood
10	chr19:44015200-44028600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:44015200-44028800	Weak transcription	Gastric	stomach
12	chr19:44015400-44028400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:44015400-44028800	Weak transcription	Fetal Thymus	thymus
14	chr19:44015400-44028800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr19:44015400-44029000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:44015400-44029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:44015400-44029400	Weak transcription	Brain Germinal Matrix	brain
18	chr19:44015400-44029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:44015600-44027000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:44015600-44027000	Weak transcription	A549	lung
21	chr19:44015600-44028400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:44015600-44028600	Weak transcription	Adipose Nuclei	Adipose
23	chr19:44015600-44028800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:44015600-44028800	Weak transcription	HepG2	liver
25	chr19:44015600-44029400	Weak transcription	Brain Anterior Caudate	brain
26	chr19:44015600-44029600	Weak transcription	Brain Substantia Nigra	brain
27	chr19:44015800-44028800	Weak transcription	Fetal Intestine Large	intestine
28	chr19:44015800-44028800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:44015800-44029000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr19:44015800-44029000	Weak transcription	Thymus	Thymus
31	chr19:44015800-44029000	Weak transcription	NHDF-Ad	bronchial
32	chr19:44015800-44029000	Weak transcription	NHLF	lung
33	chr19:44015800-44029200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:44015800-44029400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr19:44015800-44029400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:44015800-44029400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:44015800-44029400	Weak transcription	Brain Angular Gyrus	brain
38	chr19:44015800-44029400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:44015800-44029400	Weak transcription	Fetal Brain Female	brain
40	chr19:44015800-44029400	Weak transcription	Left Ventricle	heart
41	chr19:44015800-44029800	Weak transcription	Aorta	Aorta
42	chr19:44015800-44030000	Weak transcription	Ovary	ovary
43	chr19:44017000-44027000	Strong transcription	Fetal Intestine Small	intestine
44	chr19:44017200-44028800	Weak transcription	Spleen	Spleen
45	chr19:44017400-44028800	Weak transcription	Esophagus	oesophagus
46	chr19:44017600-44027200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:44017600-44029400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:44017800-44029000	Weak transcription	Fetal Muscle Leg	muscle
49	chr19:44021000-44029000	Weak transcription	Lung	lung
50	chr19:44021600-44029000	Weak transcription	HSMM	muscle

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