Variant report

Variant	rs3098393
Chromosome Location	chr19:36821209-36821210
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	POLR2A	chr19:36820950-36821365	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:36820896-36823953	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000222730	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403738	0.92[CHB][hapmap]
rs10407850	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs10416509	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs10416742	0.90[CHB][hapmap]
rs10416925	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs12459704	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs12461077	0.82[CHB][hapmap]
rs12461529	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462725	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17206379	0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2271842	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385802	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945955	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2945956	0.89[ASN][1000 genomes]
rs2945989	0.83[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2967508	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967511	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967519	0.89[ASN][1000 genomes]
rs3111555	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810326	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	0.82[CEU][hapmap];0.92[CHB][hapmap]
rs4806295	0.83[CHB][hapmap]
rs56378871	0.88[ASN][1000 genomes]
rs61706074	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112567	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112624	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112631	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112632	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62113869	0.88[ASN][1000 genomes]
rs7248731	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7251745	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs7253122	0.87[ASN][1000 genomes]
rs73043845	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73043902	0.88[ASN][1000 genomes]
rs8104241	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111860	0.82[CEU][hapmap];0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1061054	chr19:36751703-36847486	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1055260	chr19:36752221-36847486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1056850	chr19:36752663-36847486	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1064983	chr19:36752663-36847625	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1057579	chr19:36752663-36847822	Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1825146	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1837043	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv2763143	chr19:36805705-36847498	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1059568	chr19:36806475-36847864	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv1823621	chr19:36807288-36845863	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3098393	LINC00665	cis	Muscle Skeletal	GTEx
rs3098393	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs3098393	ZFP14	cis	multi-tissue	Pritchard
rs3098393	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs3098393	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs3098393	LINC00665	cis	Nerve Tibial	GTEx
rs3098393	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs3098393	LINC00665	cis	Thyroid	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36800800-36822000	Weak transcription	Psoas Muscle	Psoas
2	chr19:36805400-36822000	Weak transcription	HSMMtube	muscle
3	chr19:36806600-36822000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:36812800-36821600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr19:36813200-36821800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:36813400-36821400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:36813400-36821800	Weak transcription	Brain Substantia Nigra	brain
8	chr19:36813600-36821800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:36814800-36821400	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:36815200-36822000	Weak transcription	NHLF	lung
11	chr19:36815400-36822000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:36815800-36821400	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:36815800-36821400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:36815800-36821800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:36816200-36821400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:36816400-36821600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:36816400-36821600	Weak transcription	Fetal Heart	heart
18	chr19:36816400-36821600	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr19:36816400-36823600	ZNF genes & repeats	Liver	Liver
20	chr19:36817200-36821400	Strong transcription	Primary T cells from cord blood	blood
21	chr19:36817400-36821400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr19:36817400-36822000	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:36817600-36822000	Weak transcription	Osteobl	bone
24	chr19:36817800-36822200	Weak transcription	Placenta	Placenta
25	chr19:36818000-36821400	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr19:36818000-36821800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:36818000-36823200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr19:36818200-36821600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:36818200-36821800	Weak transcription	Adipose Nuclei	Adipose
30	chr19:36818200-36822000	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:36818200-36822000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:36818200-36822200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:36818800-36821600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:36819200-36823200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
35	chr19:36820000-36821400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
36	chr19:36820000-36821800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:36820000-36822000	Weak transcription	Ovary	ovary
38	chr19:36820000-36822200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:36820000-36822200	Weak transcription	Stomach Mucosa	stomach
40	chr19:36820000-36823600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr19:36820200-36821400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
42	chr19:36820200-36821600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:36820200-36821800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:36820200-36822200	Weak transcription	Left Ventricle	heart
45	chr19:36820200-36822200	Weak transcription	Pancreas	Pancrea
46	chr19:36820400-36821400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:36820400-36821600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:36820400-36823000	ZNF genes & repeats	Fetal Thymus	thymus
49	chr19:36820400-36823400	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr19:36820600-36821400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell

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