Variant report

Variant	rs1970121
Chromosome Location	chr9:94870152-94870153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94867851..94872295-chr9:94876110..94878962,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090054	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10512220	0.82[JPT][hapmap]
rs10739925	0.82[JPT][hapmap]
rs10761143	0.81[JPT][hapmap]
rs10820936	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.91[ASN][1000 genomes]
rs10820937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10820938	0.82[MEX][hapmap]
rs10992221	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap]
rs10992234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892268	0.82[JPT][hapmap]
rs2297568	0.82[JPT][hapmap]
rs28727560	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2895201	0.82[JPT][hapmap]
rs3750440	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs3847308	0.89[JPT][hapmap]
rs4307406	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58129324	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6479400	0.82[JPT][hapmap]
rs6479403	0.91[ASN][1000 genomes]
rs7020136	0.82[JPT][hapmap]
rs7024583	0.90[ASN][1000 genomes]
rs7029539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041193	0.82[JPT][hapmap]
rs7046540	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7848874	0.82[JPT][hapmap]
rs7852067	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7856177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7858659	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs7860518	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs7869504	0.82[JPT][hapmap]
rs7871444	0.82[JPT][hapmap]
rs7872515	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic 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	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv972418	chr9:94865248-94870773	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1970121	CDK20	cis	parietal	SCAN
rs1970121	SPTLC1	cis	parietal	SCAN
rs1970121	FBP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
2	chr9:94830800-94873800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:94840600-94872000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
5	chr9:94851400-94876600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:94857000-94875400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:94858200-94873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:94858400-94872200	Weak transcription	K562	blood
9	chr9:94858800-94873400	Weak transcription	GM12878-XiMat	blood
10	chr9:94859600-94872800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:94860400-94872000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:94860800-94872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:94860800-94873600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:94860800-94876000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:94860800-94876000	Weak transcription	Brain Substantia Nigra	brain
16	chr9:94860800-94877000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:94860800-94877200	Weak transcription	Stomach Mucosa	stomach
18	chr9:94861000-94870600	Weak transcription	Primary B cells from cord blood	blood
19	chr9:94861000-94875000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr9:94861000-94876800	Weak transcription	Fetal Kidney	kidney
21	chr9:94861200-94876000	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:94861400-94873000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:94861400-94875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:94861600-94875800	Weak transcription	Fetal Brain Male	brain
25	chr9:94861600-94877000	Weak transcription	Small Intestine	intestine
26	chr9:94863000-94870200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:94863000-94873400	Weak transcription	NHLF	lung
28	chr9:94863000-94876800	Weak transcription	HSMMtube	muscle
29	chr9:94863200-94873600	Weak transcription	Psoas Muscle	Psoas
30	chr9:94863200-94876800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:94863400-94872200	Weak transcription	NHDF-Ad	bronchial
32	chr9:94863400-94872600	Weak transcription	HUVEC	blood vessel
33	chr9:94863400-94873000	Weak transcription	HSMM	muscle
34	chr9:94863400-94873200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:94863600-94875800	Weak transcription	NHEK	skin
36	chr9:94864000-94875200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr9:94864200-94876000	Weak transcription	Hela-S3	cervix
38	chr9:94864400-94870800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:94864400-94875000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:94864400-94875000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:94864600-94873000	Weak transcription	Brain Anterior Caudate	brain
42	chr9:94864600-94875600	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:94864600-94876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:94864800-94875000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:94864800-94876200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:94865200-94870800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:94865400-94870600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:94865400-94870800	Strong transcription	Placenta	Placenta
49	chr9:94865400-94871200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:94865400-94872800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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