Variant report

Variant	rs10402740
Chromosome Location	chr19:40701181-40701182
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40700305..40703273-chr19:40704602..40706444,2	MCF-7	breast:
2	chr19:40693168..40695637-chr19:40700476..40702539,2	K562	blood:
3	chr19:40696713..40699684-chr19:40700540..40702120,2	K562	blood:
4	chr19:40699898..40702139-chr19:40702733..40704553,2	MCF-7	breast:
5	chr19:40697306..40699338-chr19:40700373..40702060,2	MCF-7	breast:
6	chr19:40697158..40699272-chr19:40700288..40703500,3	K562	blood:

Variant related genes	Relation type
ENSG00000130758	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1129156	1.00[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11668242	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs11880261	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs12971806	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975651	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs189281	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2304184	0.87[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes]
rs2356229	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339522	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs339523	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs339525	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs339526	0.89[ASW][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3730050	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs3730051	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs3746005	0.82[AMR][1000 genomes]
rs4239504	0.89[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs4257318	0.81[JPT][hapmap];0.94[MEX][hapmap]
rs4337402	0.81[JPT][hapmap]
rs4490099	0.81[JPT][hapmap];0.94[MEX][hapmap]
rs4530264	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558508	0.81[JPT][hapmap];0.93[MEX][hapmap]
rs4802070	0.87[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4802071	0.81[JPT][hapmap]
rs4802073	0.81[JPT][hapmap]
rs4802074	0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap]
rs4803320	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs56694147	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508936	0.81[JPT][hapmap]
rs7247201	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7249146	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs7250897	0.81[JPT][hapmap];0.94[MEX][hapmap]
rs7257972	0.81[JPT][hapmap]
rs7258548	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7260249	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7260517	0.81[JPT][hapmap];0.94[MEX][hapmap]
rs8100018	0.81[JPT][hapmap]
rs8102171	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs8106744	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8110888	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs969531	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs9749056	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv911698	chr19:40689580-40725304	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv911700	chr19:40695598-40725304	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10402740	C19orf47	cis	multi-tissue	Pritchard
rs10402740	CCDC97	cis	cerebellum	SCAN
rs10402740	BLVRB	cis	multi-tissue	Pritchard
rs10402740	DMRTC2	cis	parietal	SCAN
rs10402740	C19orf47	cis	lymphoblastoid	seeQTL
rs10402740	ZNF233	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40698000-40711400	Weak transcription	Fetal Kidney	kidney
2	chr19:40698400-40711200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:40698400-40714600	Weak transcription	Small Intestine	intestine
4	chr19:40698400-40715400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:40698600-40703000	Weak transcription	Fetal Intestine Small	intestine
6	chr19:40698600-40721200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:40698800-40706800	Weak transcription	HMEC	breast
8	chr19:40698800-40708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:40698800-40708600	Weak transcription	Primary B cells from cord blood	blood
10	chr19:40698800-40708600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:40698800-40708600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:40698800-40711000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:40698800-40711000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:40698800-40711000	Weak transcription	Fetal Intestine Large	intestine
15	chr19:40698800-40715600	Weak transcription	Liver	Liver
16	chr19:40698800-40719600	Weak transcription	HSMM	muscle
17	chr19:40698800-40720200	Weak transcription	NHEK	skin
18	chr19:40698800-40721400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:40698800-40722000	Weak transcription	Fetal Thymus	thymus
20	chr19:40699000-40703000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:40699000-40704000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:40699000-40706800	Weak transcription	Left Ventricle	heart
23	chr19:40699000-40707400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:40699000-40708800	Weak transcription	Gastric	stomach
25	chr19:40699000-40708800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:40699000-40709000	Weak transcription	Primary T cells from cord blood	blood
27	chr19:40699000-40709200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr19:40699000-40710400	Weak transcription	NHLF	lung
29	chr19:40699000-40711000	Weak transcription	HSMMtube	muscle
30	chr19:40699000-40716600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:40699000-40716600	Weak transcription	A549	lung
32	chr19:40699000-40720400	Weak transcription	Psoas Muscle	Psoas
33	chr19:40699000-40722200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr19:40699000-40722200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:40699000-40722400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:40699200-40701200	Enhancers	Brain Germinal Matrix	brain
37	chr19:40699200-40702400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:40699200-40703600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:40699200-40703600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:40699200-40704000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr19:40699200-40704400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:40699200-40704400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:40699200-40704400	Weak transcription	Fetal Muscle Leg	muscle
44	chr19:40699200-40705000	Weak transcription	Placenta	Placenta
45	chr19:40699200-40706200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:40699200-40708200	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:40699200-40708600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:40699200-40708600	Weak transcription	Fetal Lung	lung
49	chr19:40699200-40708600	Weak transcription	Ovary	ovary
50	chr19:40699200-40708800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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