Variant report

Variant	rs11669270
Chromosome Location	chr19:22604816-22604817
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	GABPA	chr19:22604767-22605489	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:22604777-22604899	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:22604636-22605200	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr19:22604692-22605141	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:22604732-22604843	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000269796	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10402396	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10404998	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10405295	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10406199	0.80[EUR][1000 genomes]
rs10407050	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10407485	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10409819	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10414591	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10416278	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10417380	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420149	0.84[EUR][1000 genomes]
rs10420380	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423736	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11669179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671470	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11673228	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11879678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151261	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971375	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12977311	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12978477	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12983035	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12983542	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12984257	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16999542	0.82[ASN][1000 genomes]
rs1976314	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2885037	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34187872	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34643838	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34787405	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4024619	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4932763	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71333873	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7247735	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7248242	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251413	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7255934	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100087	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8101947	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110636	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111665	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432039	chr19:22086260-22704860	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3360126	chr19:22209871-23199213	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	esv3333410	chr19:22213338-23199725	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv525240	chr19:22250912-23216667	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv432040	chr19:22316560-22704860	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3363663	chr19:22320301-23103053	Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv911439	chr19:22325391-22820798	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv911440	chr19:22325391-23216667	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
9	nsv819194	chr19:22336264-23223696	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
10	nsv911442	chr19:22338142-22801310	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
11	nsv911443	chr19:22338142-22899585	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
12	nsv911444	chr19:22338142-23198437	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
13	nsv911445	chr19:22346403-22899585	Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv819205	chr19:22346403-23199700	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
15	nsv1064071	chr19:22359491-23153773	Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv543957	chr19:22359491-23153773	Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
17	nsv932157	chr19:22359492-23192975	Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
18	esv3387241	chr19:22383621-23175441	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
19	nsv1059925	chr19:22408435-23083293	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
20	nsv1056393	chr19:22408435-23106126	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
21	esv3494593	chr19:22485508-22635008	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
22	esv3494594	chr19:22485508-22635008	Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
23	esv3360522	chr19:22485525-22634975	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
24	nsv1055896	chr19:22529565-22624042	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv1064591	chr19:22533517-22624042	Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv911447	chr19:22537862-22665616	Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11669270	ZNF98	cis	Nerve Tibial	GTEx
rs11669270	ZNF98	cis	Heart Left Ventricle	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22604200-22605400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:22604200-22605400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
3	chr19:22604200-22605400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:22604200-22605600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:22604200-22609800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:22604400-22605000	ZNF genes & repeats	Liver	Liver
7	chr19:22604400-22605200	Active TSS	Colon Smooth Muscle	Colon
8	chr19:22604400-22605200	Active TSS	Placenta Amnion	Placenta Amnion
9	chr19:22604400-22605200	Active TSS	Stomach Smooth Muscle	stomach
10	chr19:22604400-22605400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:22604400-22605400	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:22604400-22605400	Active TSS	Brain Cingulate Gyrus	brain
13	chr19:22604400-22605400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr19:22604400-22605400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:22604400-22605400	Active TSS	Fetal Kidney	kidney
16	chr19:22604400-22605400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:22604400-22605400	ZNF genes & repeats	Ovary	ovary
18	chr19:22604400-22605400	ZNF genes & repeats	Right Atrium	heart
19	chr19:22604400-22605600	Active TSS	Right Ventricle	heart
20	chr19:22604400-22605800	ZNF genes & repeats	Fetal Stomach	stomach
21	chr19:22604400-22611600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:22604600-22605000	Active TSS	Primary B cells from cord blood	blood
23	chr19:22604600-22605200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr19:22604600-22605200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:22604600-22605200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr19:22604600-22605200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:22604600-22605200	ZNF genes & repeats	Aorta	Aorta
28	chr19:22604600-22605200	Active TSS	Brain Angular Gyrus	brain
29	chr19:22604600-22605200	Active TSS	Brain Substantia Nigra	brain
30	chr19:22604600-22605200	ZNF genes & repeats	Colonic Mucosa	Colon
31	chr19:22604600-22605200	ZNF genes & repeats	Esophagus	oesophagus
32	chr19:22604600-22605200	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr19:22604600-22605200	Active TSS	Fetal Muscle Trunk	muscle
34	chr19:22604600-22605200	ZNF genes & repeats	Fetal Muscle Leg	muscle
35	chr19:22604600-22605200	ZNF genes & repeats	Lung	lung
36	chr19:22604600-22605400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:22604600-22605400	ZNF genes & repeats	Brain Anterior Caudate	brain
38	chr19:22604600-22605400	Active TSS	Brain Hippocampus Middle	brain
39	chr19:22604600-22605400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr19:22604600-22605400	Active TSS	Left Ventricle	heart
41	chr19:22604600-22605400	ZNF genes & repeats	Pancreas	Pancrea
42	chr19:22604600-22605600	Active TSS	Primary hematopoietic stem cells	blood
43	chr19:22604600-22605600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr19:22604600-22605800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr19:22604800-22605200	Active TSS	Fetal Lung	lung
46	chr19:22604800-22605200	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr19:22604800-22605200	Active TSS	HSMM	muscle
48	chr19:22604800-22605400	Active TSS	Primary T cells from cord blood	blood
49	chr19:22604800-22610800	Weak transcription	Fetal Heart	heart

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