Variant report

Variant	rs685844
Chromosome Location	chr19:21491951-21491952
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1012040	1.00[JPT][hapmap]
rs11671832	0.82[ASN][1000 genomes]
rs12151067	0.80[ASN][1000 genomes]
rs12151068	0.80[ASN][1000 genomes]
rs12971724	0.80[ASN][1000 genomes]
rs12975981	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12981869	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12984238	0.80[ASN][1000 genomes]
rs1500400	1.00[JPT][hapmap]
rs1500401	1.00[JPT][hapmap]
rs1678822	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17618715	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17618778	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1762580	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680671	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs1781863	0.81[EUR][1000 genomes]
rs1813234	1.00[CEU][hapmap]
rs1827225	0.86[ASN][1000 genomes]
rs1984771	1.00[JPT][hapmap]
rs2133820	1.00[JPT][hapmap]
rs2246914	1.00[JPT][hapmap]
rs2358984	1.00[CEU][hapmap]
rs2562448	1.00[JPT][hapmap]
rs2562457	1.00[JPT][hapmap]
rs2562458	1.00[JPT][hapmap]
rs2650779	1.00[JPT][hapmap]
rs2650780	1.00[JPT][hapmap]
rs2650781	1.00[JPT][hapmap]
rs2650783	1.00[JPT][hapmap]
rs2650791	1.00[JPT][hapmap]
rs2650794	1.00[JPT][hapmap]
rs2650799	1.00[JPT][hapmap]
rs2650845	0.86[CEU][hapmap]
rs28839521	0.80[ASN][1000 genomes]
rs2914636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914637	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928210	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34560125	0.80[ASN][1000 genomes]
rs34875588	1.00[ASN][1000 genomes]
rs35148123	0.80[ASN][1000 genomes]
rs35578515	0.85[ASN][1000 genomes]
rs35860067	1.00[ASN][1000 genomes]
rs4341872	0.87[CEU][hapmap]
rs483383	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488125	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs501647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504280	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs509540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514390	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531283	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs549882	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552039	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565406	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs566230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055133	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58121117	1.00[ASN][1000 genomes]
rs59617671	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600428	0.85[EUR][1000 genomes]
rs608002	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617186	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62107470	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107538	1.00[ASN][1000 genomes]
rs62109224	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110379	1.00[ASN][1000 genomes]
rs629548	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs635730	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs669046	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs670813	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67723811	0.80[ASN][1000 genomes]
rs7245848	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246684	1.00[ASN][1000 genomes]
rs7248700	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249636	1.00[CEU][hapmap]
rs7254436	1.00[CHB][hapmap]
rs7254762	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs73025767	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099863	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100318	1.00[JPT][hapmap]
rs8102854	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs8103411	0.85[ASN][1000 genomes]
rs8103417	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105404	1.00[ASN][1000 genomes]
rs8105629	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8107999	0.82[CHB][hapmap]
rs8110470	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113558	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs685844	ZNF738	cis	Esophagus Muscularis	GTEx
rs685844	ZNF738	cis	Thyroid	GTEx
rs685844	CTD-2561J22.5	cis	Thyroid	GTEx
rs685844	ZNF738	cis	Nerve Tibial	GTEx
rs685844	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs685844	ZNF738	cis	Adipose Subcutaneous	GTEx
rs685844	ZNF493	cis	multi-tissue	Pritchard
rs685844	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs685844	ZNF493	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
3	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
5	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:21476800-21497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:21477000-21494400	Weak transcription	Stomach Mucosa	stomach
8	chr19:21477200-21495000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:21477600-21495800	Weak transcription	HepG2	liver
10	chr19:21478000-21497400	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:21478200-21492600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:21478400-21500600	Weak transcription	Psoas Muscle	Psoas
13	chr19:21478600-21499200	Weak transcription	HMEC	breast
14	chr19:21481000-21500600	Weak transcription	NHLF	lung
15	chr19:21481200-21493000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:21481600-21500000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:21481600-21500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:21481600-21505600	Weak transcription	K562	blood
19	chr19:21481800-21492600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:21481800-21493000	Strong transcription	Dnd41	blood
21	chr19:21481800-21493400	Strong transcription	Fetal Stomach	stomach
22	chr19:21482000-21492400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:21482000-21493200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr19:21482000-21493800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:21482400-21492800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:21483200-21492800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:21483600-21493000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr19:21484000-21492200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:21484200-21492200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:21484200-21494200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:21484400-21493200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:21484600-21492400	Strong transcription	Fetal Intestine Large	intestine
34	chr19:21484800-21492000	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:21485000-21493000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:21485200-21494000	Weak transcription	NHDF-Ad	bronchial
37	chr19:21485200-21495000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr19:21485400-21508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr19:21485400-21511200	Weak transcription	Gastric	stomach
40	chr19:21485600-21497600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:21485600-21504200	Weak transcription	Pancreas	Pancrea
42	chr19:21486200-21492000	Weak transcription	Colonic Mucosa	Colon
43	chr19:21486200-21493000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:21486400-21492000	Weak transcription	Brain Germinal Matrix	brain
45	chr19:21486400-21500400	Weak transcription	Spleen	Spleen
46	chr19:21487000-21492400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:21487000-21492400	Strong transcription	Thymus	Thymus
48	chr19:21487200-21492600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:21487400-21492000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:21487400-21495200	Weak transcription	Brain Angular Gyrus	brain

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