Variant report

Variant	rs10423041
Chromosome Location	chr19:21933943-21933944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:21933920-21934179	K562	blood:	n/a	n/a
2	POLR2A	chr19:21933515-21934064	GM12892	blood:	n/a	n/a
3	WRNIP1	chr19:21933942-21933964	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:21933936-21933986	HUVEC	blood vessel:	n/a
2	chr19:21933936-21933986	HRCEpiC	kidney:	n/a
3	chr19:21933936-21933986	RPTEC	kidney:	n/a
4	chr19:21933936-21933986	MCF10A-Er-Src	breast:	n/a
5	chr19:21933936-21933986	GM12878	blood:	n/a
6	chr19:21933936-21933986	Caco-2	colon:	n/a
7	chr19:21933936-21933986	HPAEpiC	pulmonary alveolar:	n/a
8	chr19:21933936-21933986	NHDF-neo	bronchial:	n/a
9	chr19:21933936-21933986	AoSMC	blood vessel:	n/a
10	chr19:21933936-21933986	PANC-1	pancreas:	n/a
11	chr19:21933936-21933986	HL-60	blood:	n/a
12	chr19:21933936-21933986	T-47D	breast:	n/a
13	chr19:21933936-21933986	U87	brain:	n/a
14	chr19:21933936-21933986	SK-N-MC	brain:	n/a
15	chr19:21933936-21933986	HEK293	kidney:	embryo
16	chr19:21933936-21933986	HMEC	breast:	n/a
17	chr19:21933936-21933986	IMR90	lung:	fetal
18	chr19:21933936-21933986	Hepatocyte	liver:	n/a
19	chr19:21933936-21933986	MCF-7	breast:	n/a
20	chr19:21933936-21933986	NT2-D1	testis:	n/a
21	chr19:21933936-21933986	SK-N-SH_RA	brain:	n/a
22	chr19:21933936-21933986	BJ	skin:	n/a
23	chr19:21933936-21933986	GM06990	blood:	n/a
24	chr19:21933936-21933986	PrEC	prostate:	n/a
25	chr19:21933936-21933986	GM12891	blood:	n/a
26	chr19:21933936-21933986	GM12892	blood:	n/a
27	chr19:21933936-21933986	SKMC	muscle:	n/a
28	chr19:21933936-21933986	AG09319	gingival:	n/a
29	chr19:21933936-21933986	HCPEpiC	choroid plexus:	n/a
30	chr19:21933936-21933986	PFSK-1	brain:	n/a
31	chr19:21933936-21933986	ProgFib	skin:	n/a
32	chr19:21933936-21933986	NHBE	bronchial:	n/a
33	chr19:21933936-21933986	AG10803	skin:	n/a
34	chr19:21933936-21933986	GM19239	blood:	n/a
35	chr19:21933936-21933986	AG04450	lung:	fetal
36	chr19:21933936-21933986	BE2_C	brain:	n/a
37	chr19:21933936-21933986	A549	lung:	n/a
38	chr19:21933936-21933986	HRE	kidney:	n/a
39	chr19:21933936-21933986	K562	blood:	n/a
40	chr19:21933936-21933986	SK-N-SH	brain:	n/a
41	chr19:21933936-21933986	HepG2	liver:	n/a
42	chr19:21933936-21933986	ovcar-3	ovarian:	n/a
43	chr19:21933936-21933986	HCM	heart:	n/a
44	chr19:21933936-21933986	Jurkat	blood:	n/a
45	chr19:21933936-21933986	HCT-116	colon:	n/a
46	chr19:21933936-21933986	SAEC	small airway:	n/a
47	chr19:21933936-21933986	HNPCEpiC	eye:	n/a
48	chr19:21933936-21933986	H1-hESC	embryonic stem cell:	embryo
49	chr19:21933936-21933986	NH-A	brain:	n/a
50	chr19:21933936-21933986	HIPEpiC	eye:	n/a

No data

Variant related genes	Relation type
ZNF100	TF binding region
ENSG00000265084	TF binding region
ZNF100	CpG island
ENSG00000265084	CpG island

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10403795	0.84[ASN][1000 genomes]
rs10405075	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405142	0.85[ASN][1000 genomes]
rs10412225	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421342	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422982	0.81[ASN][1000 genomes]
rs11085492	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879157	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs12459784	0.80[ASN][1000 genomes]
rs12459852	0.80[ASN][1000 genomes]
rs12461775	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs3795247	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs4330044	0.87[ASN][1000 genomes]
rs4352176	0.81[ASN][1000 genomes]
rs4547465	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4613201	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808295	0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808296	0.87[ASN][1000 genomes]
rs4808297	0.82[CHB][hapmap];0.87[CHD][hapmap];0.87[ASN][1000 genomes]
rs4809175	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252777	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs7258859	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101035	0.87[ASN][1000 genomes]
rs8105002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8111464	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113652	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10423041	GDF15	cis	parietal	SCAN
rs10423041	ZNF100	cis	cerebellum	SCAN
rs10423041	ZNF100	cis	Artery Tibial	GTEx
rs10423041	HAPLN4	cis	cerebellum	SCAN
rs10423041	ZNF100	cis	Thyroid	GTEx
rs10423041	VN1R84P	cis	Nerve Tibial	GTEx
rs10423041	ZNF100	cis	parietal	SCAN
rs10423041	ZNF430	cis	cerebellum	SCAN

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	chr19:21918000-21941200	Weak transcription	Brain Angular Gyrus	brain
11	chr19:21918000-21948400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:21918800-21934400	Weak transcription	NH-A	brain
13	chr19:21919400-21943800	Strong transcription	Dnd41	blood
14	chr19:21920200-21935600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:21920200-21949200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:21920400-21948600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:21920800-21949200	Weak transcription	NHLF	lung
18	chr19:21921800-21948600	Weak transcription	Stomach Mucosa	stomach
19	chr19:21922000-21938200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:21922000-21941400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:21922000-21949400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:21922000-21949400	Weak transcription	HSMMtube	muscle
23	chr19:21922200-21934000	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:21922400-21935600	Weak transcription	HMEC	breast
25	chr19:21922400-21944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:21922400-21945000	Weak transcription	Fetal Kidney	kidney
27	chr19:21922600-21941400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:21923800-21934000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:21925000-21934200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:21925000-21935000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:21925400-21937800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:21927000-21948400	Weak transcription	HepG2	liver
33	chr19:21927400-21942600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr19:21927800-21934000	Weak transcription	Fetal Brain Male	brain
35	chr19:21928800-21937000	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:21928800-21949400	Weak transcription	Psoas Muscle	Psoas
37	chr19:21929200-21948800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr19:21929600-21936200	ZNF genes & repeats	GM12878-XiMat	blood
39	chr19:21929600-21946800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:21929600-21947400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr19:21930000-21934600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:21930200-21934400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:21930200-21936000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:21930200-21941000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:21930400-21935600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr19:21930400-21936000	Weak transcription	Right Atrium	heart
47	chr19:21930600-21941400	Weak transcription	Brain Anterior Caudate	brain
48	chr19:21930600-21944600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:21930800-21934200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:21930800-21934400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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