Variant report

Variant	rs9990198
Chromosome Location	chr3:142727334-142727335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142585981..142587495-chr3:142725915..142728856,2	MCF-7	breast:
2	chr3:142725156..142728605-chr3:142735600..142739451,5	MCF-7	breast:
3	chr3:142718194..142723452-chr3:142723791..142728813,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1107771	1.00[EUR][1000 genomes]
rs12107010	0.87[ASN][1000 genomes]
rs13321817	0.87[ASN][1000 genomes]
rs13322379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs13322528	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs13325630	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16852899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16852993	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs3821646	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58531834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764683	0.86[EUR][1000 genomes]
rs6768278	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6771415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781061	0.83[ASN][1000 genomes]
rs6782124	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797880	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806835	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990813	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72992541	0.87[ASN][1000 genomes]
rs72992555	0.86[EUR][1000 genomes]
rs7646915	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808897	0.87[ASN][1000 genomes]
rs9808965	0.87[ASN][1000 genomes]
rs9820824	0.87[ASN][1000 genomes]
rs9839114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842812	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877143	0.86[EUR][1000 genomes]
rs9881229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9881390	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882184	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883936	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142721200-142727800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:142721400-142735800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:142721600-142727400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:142721600-142728200	Weak transcription	Pancreas	Pancrea
5	chr3:142721600-142739400	Weak transcription	Lung	lung
6	chr3:142721800-142727600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:142721800-142727600	Weak transcription	Left Ventricle	heart
8	chr3:142721800-142728200	Weak transcription	Gastric	stomach
9	chr3:142721800-142730800	Weak transcription	Placenta	Placenta
10	chr3:142721800-142734800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:142721800-142736400	Weak transcription	Ovary	ovary
12	chr3:142721800-142739200	Weak transcription	Colonic Mucosa	Colon
13	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:142722000-142727400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:142722000-142727400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:142722000-142729600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:142722000-142733000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:142722000-142735800	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:142722000-142735800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:142722000-142737000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:142722000-142739000	Weak transcription	Right Ventricle	heart
22	chr3:142722000-142742400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:142722200-142728200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:142722200-142729000	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:142722200-142729200	Weak transcription	NH-A	brain
26	chr3:142722200-142729400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:142722200-142730200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:142722200-142730600	Weak transcription	Fetal Intestine Large	intestine
29	chr3:142722200-142730800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:142722200-142735800	Weak transcription	Brain Germinal Matrix	brain
31	chr3:142722200-142735800	Weak transcription	Fetal Brain Female	brain
32	chr3:142722200-142736400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:142722200-142737000	Weak transcription	Fetal Heart	heart
34	chr3:142722200-142739000	Weak transcription	Brain Angular Gyrus	brain
35	chr3:142722200-142743000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:142722400-142728400	Weak transcription	NHDF-Ad	bronchial
37	chr3:142722400-142728600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:142722400-142729600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:142722400-142730400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:142722400-142730400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:142722400-142730400	Weak transcription	HUVEC	blood vessel
42	chr3:142722400-142730600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:142722400-142731000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:142722400-142731000	Weak transcription	Adipose Nuclei	Adipose
45	chr3:142722400-142732800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:142722400-142733200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:142722400-142734600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:142722400-142735200	Weak transcription	Fetal Lung	lung
49	chr3:142722400-142735800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:142722600-142729000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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