Variant report

Variant	rs10421342
Chromosome Location	chr19:21930003-21930004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:21929838-21930101	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:21929739-21930098	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:21929830-21930030	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:21929689-21930249	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:21929704-21930013	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:21929991-21930041	T-47D	breast:	n/a
2	chr19:21929991-21930041	GM06990	blood:	n/a
3	chr19:21929991-21930041	HIPEpiC	eye:	n/a
4	chr19:21929991-21930041	ECC-1	luminal epithelium:	n/a
5	chr19:21929991-21930041	IMR90	lung:	fetal
6	chr19:21929991-21930041	CMK	blood:	n/a
7	chr19:21929991-21930041	NB4	blood:	n/a
8	chr19:21929991-21930041	HEEpiC	esophagus:	n/a
9	chr19:21929991-21930041	SK-N-MC	brain:	n/a
10	chr19:21929991-21930041	GM12892	blood:	n/a
11	chr19:21929991-21930041	GM19239	blood:	n/a
12	chr19:21929991-21930041	LNCaP	prostate:	n/a
13	chr19:21929991-21930041	Caco-2	colon:	n/a
14	chr19:21929991-21930041	HAEpiC	amniotic membrane:	n/a
15	chr19:21929991-21930041	HUVEC	blood vessel:	n/a
16	chr19:21929991-21930041	PrEC	prostate:	n/a
17	chr19:21929991-21930041	A549	lung:	n/a
18	chr19:21929991-21930041	PFSK-1	brain:	n/a
19	chr19:21929991-21930041	SKMC	muscle:	n/a
20	chr19:21929991-21930041	NH-A	brain:	n/a
21	chr19:21929991-21930041	SK-N-SH	brain:	n/a
22	chr19:21929991-21930041	HCM	heart:	n/a
23	chr19:21929991-21930041	HepG2	liver:	n/a
24	chr19:21929991-21930041	HPAEpiC	pulmonary alveolar:	n/a
25	chr19:21929991-21930041	NT2-D1	testis:	n/a
26	chr19:21929991-21930041	AG04449	skin:	fetal
27	chr19:21929991-21930041	ProgFib	skin:	n/a
28	chr19:21929991-21930041	HNPCEpiC	eye:	n/a
29	chr19:21929991-21930041	HCF	heart:	n/a
30	chr19:21929991-21930041	Jurkat	blood:	n/a
31	chr19:21929991-21930041	RPTEC	kidney:	n/a
32	chr19:21929991-21930041	AG09309	skin:	n/a
33	chr19:21929991-21930041	SK-N-SH_RA	brain:	n/a
34	chr19:21929991-21930041	HEK293	kidney:	embryo
35	chr19:21929991-21930041	AG04450	lung:	fetal
36	chr19:21929991-21930041	AG10803	skin:	n/a
37	chr19:21929991-21930041	MCF10A-Er-Src	breast:	n/a
38	chr19:21929991-21930041	NHDF-neo	bronchial:	n/a
39	chr19:21929991-21930041	HMEC	breast:	n/a
40	chr19:21929991-21930041	H1-hESC	embryonic stem cell:	embryo
41	chr19:21929991-21930041	GM12878	blood:	n/a
42	chr19:21929991-21930041	HRPEpiC	eye:	n/a
43	chr19:21929991-21930041	HRE	kidney:	n/a
44	chr19:21929991-21930041	NHBE	bronchial:	n/a
45	chr19:21929991-21930041	AG09319	gingival:	n/a
46	chr19:21929991-21930041	SAEC	small airway:	n/a
47	chr19:21929991-21930041	HRCEpiC	kidney:	n/a
48	chr19:21929991-21930041	HCT-116	colon:	n/a
49	chr19:21929991-21930041	ovcar-3	ovarian:	n/a
50	chr19:21929991-21930041	HCPEpiC	choroid plexus:	n/a

No data

Variant related genes	Relation type
ENSG00000269845	TF binding region
ENSG00000269845	CpG island

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10403795	0.84[ASN][1000 genomes]
rs10405075	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405142	0.85[ASN][1000 genomes]
rs10412225	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422982	0.81[ASN][1000 genomes]
rs10423041	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085492	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879157	0.87[ASN][1000 genomes]
rs12459784	0.80[ASN][1000 genomes]
rs12459852	0.80[ASN][1000 genomes]
rs12461775	0.80[ASN][1000 genomes]
rs3795247	0.87[ASN][1000 genomes]
rs4330044	0.87[ASN][1000 genomes]
rs4352176	0.81[ASN][1000 genomes]
rs4547465	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4613201	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808296	0.87[ASN][1000 genomes]
rs4808297	0.87[ASN][1000 genomes]
rs4809175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252777	0.87[ASN][1000 genomes]
rs7258859	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101035	0.87[ASN][1000 genomes]
rs8105002	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8111464	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113652	0.80[AFR][1000 genomes];0.99[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	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers 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	13 gene(s)	inside rSNPs	diseases
7	esv3392559	chr19:21798396-21965956	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv833783	chr19:21821406-21991838	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1815274	chr19:21825750-21981855	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv911426	chr19:21892040-21973929	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv911427	chr19:21900898-21960407	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv833784	chr19:21902647-22037153	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers 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	9 gene(s)	inside rSNPs	diseases
15	nsv578970	chr19:21906655-21973929	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv961193	chr19:21911308-21950500	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv3342879	chr19:21913482-21968857	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10421342	ZNF100	cis	Artery Tibial	GTEx
rs10421342	ZNF100	cis	Thyroid	GTEx
rs10421342	VN1R84P	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21905600-21947200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:21906200-21949200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:21908800-21948800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:21909200-21946000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:21911200-21935600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:21913400-21941200	Weak transcription	NHDF-Ad	bronchial
7	chr19:21914000-21934600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
8	chr19:21916800-21944600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:21917200-21934200	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:21917400-21933400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:21918000-21941200	Weak transcription	Brain Angular Gyrus	brain
12	chr19:21918000-21948400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:21918800-21934400	Weak transcription	NH-A	brain
14	chr19:21919400-21943800	Strong transcription	Dnd41	blood
15	chr19:21919600-21930200	Weak transcription	Brain Substantia Nigra	brain
16	chr19:21919600-21933800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:21919800-21932600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:21920200-21933600	Weak transcription	HUVEC	blood vessel
19	chr19:21920200-21935600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:21920200-21949200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:21920400-21948600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:21920800-21949200	Weak transcription	NHLF	lung
23	chr19:21921600-21930400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:21921600-21932400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:21921800-21948600	Weak transcription	Stomach Mucosa	stomach
26	chr19:21922000-21933600	Weak transcription	Spleen	Spleen
27	chr19:21922000-21938200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:21922000-21941400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr19:21922000-21949400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:21922000-21949400	Weak transcription	HSMMtube	muscle
31	chr19:21922200-21934000	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:21922400-21930200	Weak transcription	Brain Anterior Caudate	brain
33	chr19:21922400-21932200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:21922400-21935600	Weak transcription	HMEC	breast
35	chr19:21922400-21944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:21922400-21945000	Weak transcription	Fetal Kidney	kidney
37	chr19:21922600-21941400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr19:21923800-21934000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:21924200-21933800	Weak transcription	Fetal Lung	lung
40	chr19:21924800-21932400	Weak transcription	Fetal Heart	heart
41	chr19:21925000-21932600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:21925000-21933400	Weak transcription	Colonic Mucosa	Colon
43	chr19:21925000-21933600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:21925000-21933600	Weak transcription	Gastric	stomach
45	chr19:21925000-21933600	Weak transcription	Pancreas	Pancrea
46	chr19:21925000-21934200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:21925000-21935000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:21925400-21930200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:21925400-21937800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:21925800-21930800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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