Variant report

Variant	rs7257972
Chromosome Location	chr19:40841314-40841315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap]
rs10414431	0.87[ASN][1000 genomes]
rs1129156	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11668242	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880261	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12609706	0.98[ASN][1000 genomes]
rs12974529	0.85[EUR][1000 genomes]
rs12981110	0.85[EUR][1000 genomes]
rs2304184	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2304189	0.94[CHB][hapmap]
rs339526	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs3730050	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3730051	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4239504	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4239506	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4257318	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4277441	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4332845	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4337402	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4490099	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4499338	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558508	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802070	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4802071	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802074	0.83[CEU][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4803320	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6508936	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248338	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249146	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250897	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7255581	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260106	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260517	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs748236	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7508604	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8100018	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8102171	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104727	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8110888	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs969531	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9749283	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7257972	FLJ36888	cis	multi-tissue	Pritchard
rs7257972	C19orf47	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40820800-40848400	Strong transcription	Dnd41	blood
2	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:40822000-40842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:40822000-40843400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
6	chr19:40822200-40842400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:40822200-40842600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40822200-40843200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:40822200-40845400	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:40822400-40846200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:40823400-40842400	Strong transcription	Fetal Brain Female	brain
12	chr19:40823400-40845400	Strong transcription	Thymus	Thymus
13	chr19:40824000-40842200	Strong transcription	Liver	Liver
14	chr19:40824000-40842400	Strong transcription	Brain Germinal Matrix	brain
15	chr19:40824000-40842600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:40824200-40846400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:40824200-40848600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr19:40824200-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:40824400-40843000	Strong transcription	Fetal Thymus	thymus
20	chr19:40825200-40842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:40825400-40842600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr19:40825600-40842200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:40825600-40842400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:40825800-40841600	Strong transcription	Right Ventricle	heart
25	chr19:40825800-40842200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:40825800-40842200	Strong transcription	Adipose Nuclei	Adipose
27	chr19:40825800-40842400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:40825800-40842400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:40825800-40842400	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:40825800-40842600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:40825800-40842600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:40825800-40845400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:40826000-40842200	Strong transcription	Gastric	stomach
34	chr19:40826000-40842400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:40826000-40842400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr19:40826000-40842400	Strong transcription	Fetal Intestine Large	intestine
37	chr19:40826000-40842400	Strong transcription	Left Ventricle	heart
38	chr19:40826000-40842400	Strong transcription	Ovary	ovary
39	chr19:40826400-40842200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:40826400-40842400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:40826400-40843000	Strong transcription	Primary T cells from cord blood	blood
42	chr19:40826400-40847400	Weak transcription	Right Atrium	heart
43	chr19:40826600-40842000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:40826600-40842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:40826600-40842800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr19:40826600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:40826800-40842200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:40826800-40842400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:40826800-40842800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:40827600-40845000	Strong transcription	GM12878-XiMat	blood

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