Variant report

Variant	rs3803919
Chromosome Location	chr19:18311111-18311112
allele	C/T
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	JUND	chr19:18311083-18311302	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18301873..18308921-chr19:18309874..18315133,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268650	TF binding region
ENSG00000254858	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1045747	0.89[JPT][hapmap]
rs1046565	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11881258	0.93[EUR][1000 genomes]
rs12460619	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12461021	0.92[EUR][1000 genomes]
rs12462801	0.93[EUR][1000 genomes]
rs17683509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs17683539	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2049050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229228	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs2271882	0.86[CHB][hapmap]
rs4458132	0.91[EUR][1000 genomes]
rs4808118	0.89[JPT][hapmap]
rs4808768	0.87[EUR][1000 genomes]
rs55650549	0.93[EUR][1000 genomes]
rs62120367	0.82[EUR][1000 genomes]
rs62120368	0.92[EUR][1000 genomes]
rs62120382	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62120383	0.93[EUR][1000 genomes]
rs62120385	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62120388	0.95[EUR][1000 genomes]
rs62120393	0.91[EUR][1000 genomes]
rs7245576	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs7246274	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7259695	0.88[EUR][1000 genomes]
rs8100626	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs8104010	0.91[EUR][1000 genomes]
rs8109807	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS 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	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
11	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
13	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
14	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
15	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	nsv911261	chr19:18288947-18311199	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
17	nsv911262	chr19:18288947-18312453	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
18	nsv828470	chr19:18289598-18311602	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
19	nsv828471	chr19:18293567-18311602	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
20	nsv819691	chr19:18294153-18312275	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
21	nsv911263	chr19:18309365-18324329	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv911264	chr19:18309365-18369644	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3803919	KIAA1683	cis	cerebellum	SCAN
rs3803919	ZNF738	cis	parietal	SCAN
rs3803919	ZNF429	cis	cerebellum	SCAN
rs3803919	OR7A10	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18305200-18314000	Weak transcription	HSMMtube	muscle
2	chr19:18305400-18312800	Weak transcription	Fetal Brain Male	brain
3	chr19:18305400-18313800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:18305400-18313800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:18305400-18314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:18305400-18314200	Weak transcription	Small Intestine	intestine
7	chr19:18305600-18311600	Strong transcription	Fetal Intestine Small	intestine
8	chr19:18305600-18313400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:18305600-18313400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:18305600-18313800	Weak transcription	Psoas Muscle	Psoas
11	chr19:18305600-18313800	Weak transcription	A549	lung
12	chr19:18305600-18313800	Weak transcription	NH-A	brain
13	chr19:18305600-18314000	Weak transcription	HSMM	muscle
14	chr19:18306000-18311400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:18306000-18311400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:18306000-18311400	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:18306000-18311600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:18306000-18311600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:18306000-18311600	Strong transcription	Ovary	ovary
20	chr19:18306000-18312000	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:18306000-18313000	Strong transcription	Brain Cingulate Gyrus	brain
22	chr19:18306000-18313400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:18306000-18313600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:18306000-18313600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:18306000-18313600	Strong transcription	Fetal Stomach	stomach
26	chr19:18306000-18313600	Weak transcription	Stomach Mucosa	stomach
27	chr19:18306000-18313800	Weak transcription	HMEC	breast
28	chr19:18306200-18311600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:18306200-18311800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:18306200-18313400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:18306200-18313400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr19:18306200-18313400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:18306400-18311400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:18306400-18313000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:18306400-18313400	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr19:18306400-18313400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:18306600-18311400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:18306600-18311400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr19:18306600-18311600	Strong transcription	Brain Anterior Caudate	brain
40	chr19:18306600-18311800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:18306600-18311800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:18306600-18313000	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr19:18306800-18311200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:18306800-18311600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr19:18306800-18311600	Strong transcription	Fetal Muscle Leg	muscle
46	chr19:18306800-18311600	Strong transcription	GM12878-XiMat	blood
47	chr19:18306800-18311800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:18306800-18312800	Strong transcription	Fetal Brain Female	brain
49	chr19:18306800-18313200	Strong transcription	Colon Smooth Muscle	Colon
50	chr19:18307000-18313200	Strong transcription	Stomach Smooth Muscle	stomach

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