Variant report

Variant	rs10412225
Chromosome Location	chr19:21944450-21944451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:21940917..21942480-chr19:21942813..21945738,3	K562	blood:
2	chr19:21942889..21945797-chr19:21949432..21951417,3	MCF-7	breast:
3	chr19:21942882..21944718-chr19:21948688..21951002,2	K562	blood:
4	chr19:21942882..21946076-chr19:21948688..21950754,3	K562	blood:

Variant related genes	Relation type
ENSG00000197020	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10403795	0.83[ASN][1000 genomes]
rs10405075	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405142	0.84[ASN][1000 genomes]
rs10421113	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421342	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10422982	0.80[ASN][1000 genomes]
rs10423041	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11085492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879157	0.86[ASN][1000 genomes]
rs12459784	0.81[ASN][1000 genomes]
rs12459852	0.81[ASN][1000 genomes]
rs12461775	0.81[ASN][1000 genomes]
rs3795247	0.86[ASN][1000 genomes]
rs4330044	0.86[ASN][1000 genomes]
rs4352176	0.80[ASN][1000 genomes]
rs4547465	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4613201	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808295	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808296	0.86[ASN][1000 genomes]
rs4808297	0.86[ASN][1000 genomes]
rs4809175	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252777	0.86[ASN][1000 genomes]
rs7258859	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101035	0.86[ASN][1000 genomes]
rs8105002	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8111464	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113652	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
18	nsv1059457	chr19:21940891-21999025	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10412225	ZNF100	cis	Artery Tibial	GTEx
rs10412225	ZNF100	cis	Thyroid	GTEx
rs10412225	VN1R84P	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 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	chr19:21916800-21944600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:21918000-21948400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:21920200-21949200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:21920400-21948600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:21920800-21949200	Weak transcription	NHLF	lung
10	chr19:21921800-21948600	Weak transcription	Stomach Mucosa	stomach
11	chr19:21922000-21949400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:21922000-21949400	Weak transcription	HSMMtube	muscle
13	chr19:21922400-21945000	Weak transcription	Fetal Kidney	kidney
14	chr19:21927000-21948400	Weak transcription	HepG2	liver
15	chr19:21928800-21949400	Weak transcription	Psoas Muscle	Psoas
16	chr19:21929200-21948800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr19:21929600-21946800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:21929600-21947400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:21930600-21944600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:21933800-21948600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:21933800-21949400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:21934600-21945400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr19:21934600-21949200	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:21934800-21948600	Weak transcription	Fetal Heart	heart
25	chr19:21935400-21949400	Weak transcription	Brain Substantia Nigra	brain
26	chr19:21935800-21948600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:21936200-21948400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:21936200-21949400	Weak transcription	Colonic Mucosa	Colon
29	chr19:21936400-21946200	Weak transcription	Pancreas	Pancrea
30	chr19:21936400-21948600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:21936800-21944600	Weak transcription	HUVEC	blood vessel
32	chr19:21937800-21948800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
33	chr19:21938000-21946000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:21938000-21947000	ZNF genes & repeats	Fetal Brain Female	brain
35	chr19:21938000-21947400	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr19:21938000-21948600	Strong transcription	Fetal Intestine Large	intestine
37	chr19:21938200-21948800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:21938400-21947600	Strong transcription	Thymus	Thymus
39	chr19:21938600-21947200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr19:21938600-21948200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:21938600-21948400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr19:21938800-21948200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:21938800-21948400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:21939800-21946000	Strong transcription	Brain Hippocampus Middle	brain
45	chr19:21939800-21947600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:21939800-21947800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:21939800-21948800	Strong transcription	Fetal Stomach	stomach
48	chr19:21940000-21945800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:21940000-21946000	Strong transcription	Adipose Nuclei	Adipose
50	chr19:21940000-21948000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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