Variant report

Variant	rs12712123
Chromosome Location	chr2:98407667-98407668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98406044..98408810-chr2:98414530..98416277,2	MCF-7	breast:
2	chr2:98407471..98409052-chr2:98413591..98415122,2	MCF-7	breast:
3	chr2:98397492..98399885-chr2:98406316..98408049,2	K562	blood:
4	chr2:98403775..98408047-chr2:98409858..98412434,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10176201	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10200949	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10211231	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1071885	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865055	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11123924	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123949	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123966	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11690482	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11693874	0.80[ASN][1000 genomes]
rs11888323	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11899171	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13003978	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13006817	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13008503	0.83[ASN][1000 genomes]
rs13010946	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022778	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13034644	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13405546	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466020	0.94[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1466924	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1503200	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1922280	0.90[ASN][1000 genomes]
rs1922282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017028	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2091772	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2100058	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141862	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279826	0.80[ASN][1000 genomes]
rs2305142	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2309316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2309317	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2309356	0.83[ASN][1000 genomes]
rs3762593	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4560167	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5865	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543109	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6543161	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543177	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543202	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6543210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707924	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709571	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6712517	0.83[CEU][hapmap]
rs6719556	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723466	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6723653	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6744331	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748809	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6748927	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.99[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7561104	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562695	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7574437	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577886	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582664	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586210	0.80[ASN][1000 genomes]
rs7598116	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7602412	0.80[ASN][1000 genomes]
rs7605180	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs930607	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308862	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs956696	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9973416	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12712123	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs12712123	ZAP70	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98368600-98413000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:98377400-98408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:98377400-98410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:98378600-98421400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:98382800-98419800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:98383000-98408600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:98383200-98408800	Weak transcription	Fetal Brain Male	brain
8	chr2:98383200-98420200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:98387800-98408000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:98387800-98408000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:98387800-98438200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:98388000-98407800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:98388000-98408600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:98389000-98408200	Weak transcription	NH-A	brain
15	chr2:98390200-98408000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:98391400-98408000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:98392200-98409200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:98392400-98407800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:98392400-98407800	Weak transcription	Brain Angular Gyrus	brain
20	chr2:98392400-98407800	Weak transcription	HSMMtube	muscle
21	chr2:98392400-98408800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:98392400-98415600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:98392400-98418600	Weak transcription	Fetal Kidney	kidney
24	chr2:98392600-98408000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:98393800-98407800	Weak transcription	Brain Anterior Caudate	brain
26	chr2:98393800-98409000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:98394200-98415000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:98396200-98408000	Weak transcription	NHEK	skin
29	chr2:98398800-98421000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:98399000-98409200	Weak transcription	Small Intestine	intestine
31	chr2:98399600-98429600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:98401400-98422600	Strong transcription	Primary B cells from cord blood	blood
33	chr2:98401600-98422400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:98402000-98411600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:98402000-98416600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:98402000-98423200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:98402000-98440400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:98402200-98412000	Strong transcription	Fetal Intestine Large	intestine
39	chr2:98402200-98422200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:98402200-98422600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:98402400-98410000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:98402400-98410000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:98402400-98410000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr2:98402400-98410000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:98402400-98410200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:98402400-98410200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr2:98402400-98410400	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:98402400-98410600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:98402400-98411400	Strong transcription	Fetal Stomach	stomach
50	chr2:98402400-98411800	Strong transcription	Primary T cells fromperipheralblood	blood

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