Variant report

Variant	rs2116888
Chromosome Location	chr19:19978757-19978758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19975991..19979508-chr19:19981059..19984923,4	K562	blood:
2	chr19:19977897..19980887-chr19:19981343..19982993,2	K562	blood:
3	chr19:19976692..19979119-chr19:20011140..20013486,2	K562	blood:

Variant related genes	Relation type
ENSG00000184635	Chromatin interaction
ENSG00000270270	Chromatin interaction
ENSG00000267268	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10415754	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304169	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28888982	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250258	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking 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 miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription 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	47 gene(s)	inside rSNPs	diseases
14	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	53 gene(s)	inside rSNPs	diseases
15	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic 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	23 gene(s)	inside rSNPs	diseases
17	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2116888	ZNF682	cis	Muscle Skeletal	GTEx
rs2116888	ZNF253	cis	Nerve Tibial	GTEx
rs2116888	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19975800-19978800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:19976000-19978800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:19976000-19978800	Active TSS	Duodenum Mucosa	Duodenum
4	chr19:19976000-19979000	Active TSS	Brain Angular Gyrus	brain
5	chr19:19976000-19979200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr19:19976000-19979200	Active TSS	Right Atrium	heart
7	chr19:19976200-19979200	Active TSS	Brain Germinal Matrix	brain
8	chr19:19976200-19979200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr19:19976200-19979200	Active TSS	Stomach Smooth Muscle	stomach
10	chr19:19976400-19979200	Active TSS	K562	blood
11	chr19:19976400-19979600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:19976600-19978800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:19976600-19978800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr19:19976600-19978800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:19976600-19978800	Active TSS	Fetal Brain Male	brain
16	chr19:19976600-19978800	Active TSS	Fetal Lung	lung
17	chr19:19976600-19979000	Active TSS	HSMMtube	muscle
18	chr19:19976600-19979200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr19:19976600-19979200	Active TSS	Brain Anterior Caudate	brain
20	chr19:19976600-19979200	Active TSS	Brain Cingulate Gyrus	brain
21	chr19:19976600-19979600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:19976600-19979600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:19976600-19979600	Active TSS	Fetal Brain Female	brain
24	chr19:19976600-19979800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr19:19976600-19980200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:19977600-19995600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:19977600-20006800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:19977800-19979600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:19977800-19993200	Weak transcription	Spleen	Spleen
30	chr19:19978000-19978800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr19:19978000-19979800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:19978000-19980000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr19:19978000-19982000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:19978000-19982600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:19978200-19978800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:19978200-19979000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:19978200-19979400	ZNF genes & repeats	GM12878-XiMat	blood
38	chr19:19978200-19980400	Transcr. at gene 5' and 3'	Dnd41	blood
39	chr19:19978200-19993600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:19978400-19979000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr19:19978400-19979200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:19978400-19979400	Enhancers	Primary B cells from cord blood	blood
43	chr19:19978400-19979400	Enhancers	Brain Substantia Nigra	brain
44	chr19:19978400-19979600	Enhancers	Primary B cells from peripheral blood	blood
45	chr19:19978400-19979600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr19:19978400-19981000	Weak transcription	Small Intestine	intestine
47	chr19:19978400-19982000	Weak transcription	Gastric	stomach
48	chr19:19978400-19983200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr19:19978400-19984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:19978400-19984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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