Variant report

Variant	rs2125089
Chromosome Location	chr12:10760380-10760381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:10753486..10755683-chr12:10758710..10760560,2	MCF-7	breast:
2	chr12:10758501..10762466-chr12:10825549..10828463,4	MCF-7	breast:
3	chr12:10759828..10762348-chr12:10763400..10769792,9	K562	blood:
4	chr12:10757768..10761323-chr12:10763648..10767654,5	MCF-7	breast:
5	chr12:10752173..10753763-chr12:10760040..10762966,2	MCF-7	breast:
6	chr12:10760140..10761082-chr12:10826372..10827064,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256667	Chromatin interaction
ENSG00000111196	Chromatin interaction
ENSG00000060140	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1026445	1.00[CHB][hapmap]
rs1026446	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1052871	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10772333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10772335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs10845182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs2011295	0.89[GIH][hapmap]
rs2125090	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2198965	0.92[EUR][1000 genomes]
rs2219383	0.93[CEU][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs2243823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[MEX][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417908	0.85[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs2682484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3463	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3947920	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4763210	0.91[EUR][1000 genomes]
rs4763211	0.93[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4763562	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[ASN][1000 genomes]
rs4763563	1.00[ASN][1000 genomes]
rs6488312	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6488313	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7308433	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316237	1.00[CEU][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs7965803	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs7976279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897879	0.82[AMR][1000 genomes]
rs897881	0.87[AMR][1000 genomes]
rs953248	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv516351	chr12:10759489-10764045	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2125089	HEBP1	cis	cerebellum	SCAN
rs2125089	KLRC2	cis	cerebellum	SCAN
rs2125089	KLRC3	cis	cerebellum	SCAN
rs2125089	KLRC4	cis	parietal	SCAN
rs2125089	GPRC5A	cis	cerebellum	SCAN
rs2125089	KLRC2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10725600-10765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:10730000-10762000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:10730600-10764800	Weak transcription	Lung	lung
5	chr12:10731600-10760800	Weak transcription	Fetal Brain Female	brain
6	chr12:10732200-10761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:10732200-10764800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:10732400-10764200	Weak transcription	Pancreas	Pancrea
9	chr12:10734000-10764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:10734000-10764600	Weak transcription	Thymus	Thymus
11	chr12:10734200-10762200	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:10734200-10764000	Weak transcription	Fetal Stomach	stomach
13	chr12:10734400-10764600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:10735200-10764600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:10735400-10764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:10738800-10764000	Weak transcription	Fetal Intestine Small	intestine
17	chr12:10739400-10761400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:10742000-10761200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:10742600-10764600	Weak transcription	Small Intestine	intestine
20	chr12:10742800-10764800	Weak transcription	Psoas Muscle	Psoas
21	chr12:10743400-10765400	Weak transcription	Gastric	stomach
22	chr12:10744000-10765200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:10744000-10765400	Weak transcription	Aorta	Aorta
24	chr12:10744200-10764000	Weak transcription	Ovary	ovary
25	chr12:10744200-10764600	Weak transcription	HSMMtube	muscle
26	chr12:10744200-10765400	Weak transcription	Esophagus	oesophagus
27	chr12:10747000-10764800	Weak transcription	Right Ventricle	heart
28	chr12:10748000-10762400	Weak transcription	Hela-S3	cervix
29	chr12:10748400-10764600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:10749400-10764800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:10750200-10761400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:10751800-10764000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:10752000-10760400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:10752000-10762600	Weak transcription	HepG2	liver
35	chr12:10752200-10764800	Weak transcription	Colonic Mucosa	Colon
36	chr12:10752400-10764600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:10753200-10761400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:10753200-10762800	Strong transcription	Primary B cells from cord blood	blood
39	chr12:10753400-10762600	Strong transcription	Dnd41	blood
40	chr12:10753600-10765400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:10754000-10764400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:10754200-10761000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:10755000-10761400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:10755000-10763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:10755200-10762600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:10755200-10764600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:10755400-10763000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:10755800-10764800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:10756200-10763000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:10756200-10763000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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