Variant report

Variant	rs862234
Chromosome Location	chr19:37728002-37728003
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37708605..37710654-chr19:37725265..37728083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188283	Chromatin interaction
ENSG00000245680	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1234250	0.84[CEU][hapmap]
rs17707446	1.00[YRI][hapmap]
rs185368	0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs185369	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs2385180	0.82[ASW][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs2431992	0.80[CHB][hapmap]
rs256733	0.82[ASW][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs256735	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs320876	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs320881	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs320887	0.92[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs320888	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs502546	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs7254009	1.00[ASW][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs7257135	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
6	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS 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 target site	17 gene(s)	inside rSNPs	diseases
9	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv961287	chr19:37708789-37742224	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
12	nsv960833	chr19:37715348-37733416	Strong transcription ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	nsv9717	chr19:37721760-37796698	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs862234	AC012309.5	cis	Heart Left Ventricle	GTEx
rs862234	AC012309.5	cis	Thyroid	GTEx
rs862234	PAK4	cis	cerebellum	SCAN
rs862234	AC012309.5	cis	Artery Tibial	GTEx
rs862234	SIPA1L3	cis	cerebellum	SCAN
rs862234	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs862234	ARHGEF1	cis	cerebellum	SCAN
rs862234	CCDC97	cis	cerebellum	SCAN
rs862234	PLEKHG2	cis	cerebellum	SCAN
rs862234	LINC00665	cis	Heart Left Ventricle	GTEx
rs862234	HKR1	cis	Whole Blood	GTEx
rs862234	PVR	cis	parietal	SCAN
rs862234	AC012309.5	cis	Muscle Skeletal	GTEx
rs862234	ZNF781	cis	Thyroid	GTEx
rs862234	POU2F2	cis	parietal	SCAN
rs862234	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs862234	HIPK4	cis	parietal	SCAN
rs862234	AC012309.5	cis	Esophagus Muscularis	GTEx
rs862234	AC012309.5	cis	Esophagus Mucosa	GTEx
rs862234	ZNF585B	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37710000-37728600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37710200-37728600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:37710400-37744200	ZNF genes & repeats	Liver	Liver
4	chr19:37711000-37737000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:37711000-37737800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37711200-37738200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:37713400-37728400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:37715200-37736600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:37715200-37740400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:37715400-37732600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr19:37715400-37738400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:37715600-37736000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr19:37715800-37738000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr19:37716000-37736000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr19:37716200-37731600	Strong transcription	Brain Germinal Matrix	brain
16	chr19:37718400-37735600	ZNF genes & repeats	Primary T cells from cord blood	blood
17	chr19:37718400-37735600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr19:37720800-37735400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
19	chr19:37720800-37735400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
20	chr19:37720800-37736200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
21	chr19:37720800-37736400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:37720800-37738600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr19:37720800-37740200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:37720800-37740400	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr19:37722600-37737800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:37723200-37729200	Strong transcription	Osteobl	bone
27	chr19:37724000-37737000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:37724200-37732600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:37724200-37737000	ZNF genes & repeats	Ovary	ovary
30	chr19:37724400-37732400	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr19:37724400-37732600	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr19:37724400-37734400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:37724400-37735400	ZNF genes & repeats	Small Intestine	intestine
34	chr19:37724400-37736600	ZNF genes & repeats	Psoas Muscle	Psoas
35	chr19:37724600-37732600	ZNF genes & repeats	Lung	lung
36	chr19:37724800-37728200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:37724800-37735400	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr19:37724800-37736600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:37724800-37738600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:37725000-37729000	ZNF genes & repeats	HMEC	breast
41	chr19:37725000-37729400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:37725000-37732000	Strong transcription	Brain Substantia Nigra	brain
43	chr19:37725000-37734600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
44	chr19:37725000-37734600	ZNF genes & repeats	GM12878-XiMat	blood
45	chr19:37725000-37736000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:37725000-37736400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
47	chr19:37725000-37737200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
48	chr19:37725000-37737200	ZNF genes & repeats	A549	lung
49	chr19:37725000-37737400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:37725000-37737600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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