Variant report

Variant	rs9880211
Chromosome Location	chr3:136107549-136107550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136106528..136109586-chr3:136469250..136472144,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12695645	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12695649	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs13072038	0.85[EUR][1000 genomes]
rs13092193	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13316214	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13321721	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs13326151	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs1604793	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17200216	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17298525	1.00[CEU][hapmap]
rs17364492	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs28634226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28718456	0.81[EUR][1000 genomes]
rs34031772	0.88[EUR][1000 genomes]
rs34135127	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs34168675	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34282798	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34324561	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34757183	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34913797	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35320690	0.94[GIH][hapmap];1.00[YRI][hapmap]
rs35375192	0.81[GIH][hapmap]
rs6768743	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs6769762	0.94[GIH][hapmap]
rs6771002	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6796523	0.89[EUR][1000 genomes]
rs6806123	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9810051	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9812579	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9813115	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9813691	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9818056	0.81[EUR][1000 genomes]
rs9818536	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9820621	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823373	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9832813	0.83[GIH][hapmap];0.92[MEX][hapmap]
rs9837158	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9841529	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9844666	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs9857966	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9866840	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870825	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9872178	0.89[EUR][1000 genomes]
rs9878078	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9883189	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9880211	ERICH1	trans	parietal	SCAN
rs9880211	HCST	trans	parietal	SCAN
rs9880211	PPP2R3A	cis	parietal	SCAN
rs9880211	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
5	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
6	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel
7	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
13	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:136075400-136108000	Weak transcription	Fetal Brain Female	brain
16	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
17	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:136081200-136118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:136083200-136111400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:136084400-136123200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:136085600-136116400	Weak transcription	Fetal Intestine Large	intestine
22	chr3:136085800-136116400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:136085800-136139200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:136086000-136112200	Weak transcription	Liver	Liver
26	chr3:136086000-136128400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:136086000-136136000	Weak transcription	HSMM	muscle
28	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:136086400-136116800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:136088400-136121200	Weak transcription	Thymus	Thymus
31	chr3:136092200-136108000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:136093200-136117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:136094600-136115800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:136095600-136116200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:136095600-136117200	Weak transcription	Placenta	Placenta
36	chr3:136095600-136121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:136095600-136132400	Weak transcription	Left Ventricle	heart
38	chr3:136095600-136132600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:136095600-136134400	Weak transcription	Adipose Nuclei	Adipose
40	chr3:136095600-136137800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:136095800-136116600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:136095800-136118800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:136095800-136121200	Weak transcription	Fetal Thymus	thymus
44	chr3:136095800-136122800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:136095800-136131600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:136095800-136135200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:136095800-136139200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:136096000-136115800	Weak transcription	Dnd41	blood
49	chr3:136096000-136132800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:136096000-136138200	Weak transcription	Lung	lung

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