Variant report

Variant	rs248946
Chromosome Location	chr19:19888416-19888417
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	CTCF	chr19:19888340-19888490	HFF-Myc	foreskin:	n/a	n/a
2	CTCF	chr19:19888380-19888530	AG09309	skin:	n/a	chr19:19888520-19888529
3	HCFC1	chr19:19886407-19888705	Hela-S3	cervix:	n/a	n/a
4	SREBP1	chr19:19886186-19888557	GM12878	blood:	n/a	chr19:19887863-19887877
5	KAP1	chr19:19886924-19889014	HEK293	kidney:	n/a	n/a
6	MXI1	chr19:19886113-19889151	SK-N-SH	brain:	n/a	chr19:19886836-19886845

Variant related genes	Relation type
LINC00663	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10404296	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10412885	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12710110	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16996360	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248930	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248931	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248932	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248933	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248934	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248936	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248942	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248948	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248949	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248951	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248952	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248954	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762190	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808216	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4808989	0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808995	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246727	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256535	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106100	0.87[EUR][1000 genomes]
rs8109240	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111421	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS 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
7	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs248946	ZNF506	cis	normal skin	skin_eQTL
rs248946	ZNF682	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19886200-19888600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:19886200-19888600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19886200-19888600	Active TSS	A549	lung
4	chr19:19886400-19888600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:19886400-19888600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:19886400-19888600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:19886400-19888800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:19886400-19889000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:19886600-19888600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:19886600-19889000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:19886800-19888600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:19886800-19888600	Active TSS	Fetal Intestine Small	intestine
13	chr19:19887000-19888600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr19:19887000-19888600	Active TSS	Colonic Mucosa	Colon
15	chr19:19887600-19888600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr19:19887600-19888600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr19:19887600-19888600	Flanking Active TSS	Liver	Liver
18	chr19:19887800-19888600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr19:19887800-19888600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr19:19887800-19888600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:19887800-19888600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:19887800-19888600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:19887800-19888600	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr19:19887800-19888600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr19:19887800-19888600	Flanking Active TSS	Fetal Brain Female	brain
26	chr19:19887800-19888600	Flanking Active TSS	Hela-S3	cervix
27	chr19:19887800-19888800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr19:19887800-19888800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr19:19888000-19888600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:19888000-19888600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:19888000-19888600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:19888000-19888600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:19888000-19888600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr19:19888000-19888600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:19888000-19888600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:19888000-19888600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr19:19888000-19888600	Enhancers	Small Intestine	intestine
38	chr19:19888000-19888600	Flanking Active TSS	HMEC	breast
39	chr19:19888000-19888600	Flanking Active TSS	Osteobl	bone
40	chr19:19888000-19888800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr19:19888000-19888800	Enhancers	Spleen	Spleen
42	chr19:19888000-19889000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:19888000-19889000	Flanking Active TSS	Dnd41	blood
44	chr19:19888000-19889200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:19888000-19889200	Enhancers	Gastric	stomach
46	chr19:19888000-19892600	Weak transcription	Esophagus	oesophagus
47	chr19:19888000-19897000	Weak transcription	Left Ventricle	heart
48	chr19:19888000-19897200	Weak transcription	Aorta	Aorta
49	chr19:19888000-19899600	Weak transcription	Ovary	ovary
50	chr19:19888200-19888600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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