Variant report

Variant	rs10880872
Chromosome Location	chr12:46344979-46344980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46344593..46346817-chr12:46380170..46382084,2	MCF-7	breast:
2	chr12:46344313..46347392-chr12:46347500..46350157,3	MCF-7	breast:
3	chr12:46341596..46343310-chr12:46343404..46346172,2	K562	blood:

Variant related genes	Relation type
ENSG00000139218	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10880868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183212	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12580303	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12828693	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1978598	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7298844	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7310939	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7316454	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv3439887	chr12:46337377-46370366	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880872	SFRS2IP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46312200-46348600	Strong transcription	Dnd41	blood
3	chr12:46314600-46345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:46319200-46362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:46322600-46360200	Weak transcription	Fetal Brain Male	brain
6	chr12:46324400-46351600	Weak transcription	Psoas Muscle	Psoas
7	chr12:46326600-46360400	Weak transcription	Small Intestine	intestine
8	chr12:46328800-46345200	Strong transcription	HSMM	muscle
9	chr12:46329200-46351800	Weak transcription	Fetal Heart	heart
10	chr12:46329600-46348800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:46329800-46371000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:46330400-46358800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:46331000-46347000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr12:46331400-46351200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:46331600-46345000	Strong transcription	Placenta	Placenta
16	chr12:46333600-46345200	Strong transcription	Fetal Thymus	thymus
17	chr12:46333600-46345200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:46336400-46351600	Weak transcription	Aorta	Aorta
19	chr12:46338200-46356000	Weak transcription	Fetal Brain Female	brain
20	chr12:46338800-46359800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:46338800-46360000	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:46338800-46360000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:46340000-46356600	Weak transcription	Brain Anterior Caudate	brain
24	chr12:46341600-46355200	Weak transcription	HMEC	breast
25	chr12:46341800-46345200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:46341800-46365600	Weak transcription	K562	blood
27	chr12:46342000-46346600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:46342000-46347800	Weak transcription	Fetal Intestine Small	intestine
29	chr12:46342000-46348200	Weak transcription	Thymus	Thymus
30	chr12:46342000-46349000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:46342000-46355200	Weak transcription	Esophagus	oesophagus
32	chr12:46342000-46356600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:46342000-46358400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:46342000-46360400	Weak transcription	Ovary	ovary
35	chr12:46342000-46360800	Weak transcription	Lung	lung
36	chr12:46342000-46362400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:46342000-46362400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:46342000-46362400	Weak transcription	Pancreas	Pancrea
39	chr12:46342000-46363000	Weak transcription	Fetal Stomach	stomach
40	chr12:46342000-46364000	Weak transcription	Gastric	stomach
41	chr12:46342200-46351600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:46342200-46351600	Weak transcription	Left Ventricle	heart
43	chr12:46342200-46353600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:46342200-46356200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:46342200-46356600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:46342200-46358800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:46342200-46359200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:46342200-46359800	Weak transcription	NHLF	lung
49	chr12:46342200-46360200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:46342200-46361000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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