Variant report

Variant	rs2309317
Chromosome Location	chr2:98414417-98414418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:98414402-98414465	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98407471..98409052-chr2:98413591..98415122,2	MCF-7	breast:
2	chr2:98414101..98415946-chr2:98420094..98421942,2	MCF-7	breast:

Variant related genes	Relation type
TMEM131	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10176201	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10182941	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10200949	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10211231	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1071885	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10865055	0.85[AFR][1000 genomes]
rs11123924	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123949	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123966	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11690482	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11888323	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11899171	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712123	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712174	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13003978	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13006817	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13010946	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13022778	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13034644	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1317178	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13405546	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1466020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1466924	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1503200	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1922280	0.87[ASN][1000 genomes]
rs1922282	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2017028	0.85[AFR][1000 genomes]
rs2091772	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2100058	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141862	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2309316	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762593	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4274643	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4560167	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5865	0.90[ASN][1000 genomes]
rs6543108	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543109	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543161	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6543177	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6543202	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6543210	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6707924	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6709571	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6710813	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6719556	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6723466	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6723653	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6744331	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6748809	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6748927	0.95[ASN][1000 genomes]
rs7558931	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7561104	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7562695	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7567397	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574437	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7577886	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7582664	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7598116	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7602412	0.81[AFR][1000 genomes]
rs7605180	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs930607	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9308862	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs956696	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9973416	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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
rs2309317	ZAP70	cis	Nerve Tibial	GTEx
rs2309317	TMEM131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98378600-98421400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:98382800-98419800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:98383200-98420200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:98387800-98438200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:98392400-98415600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:98392400-98418600	Weak transcription	Fetal Kidney	kidney
7	chr2:98394200-98415000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:98398800-98421000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:98399600-98429600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:98401400-98422600	Strong transcription	Primary B cells from cord blood	blood
11	chr2:98401600-98422400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:98402000-98416600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:98402000-98423200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:98402000-98440400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:98402200-98422200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:98402200-98422600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:98402400-98428600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:98402600-98422200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:98402600-98422600	Strong transcription	Liver	Liver
20	chr2:98403200-98422400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:98403600-98422600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
23	chr2:98406000-98414800	Weak transcription	Fetal Heart	heart
24	chr2:98406200-98427200	Weak transcription	K562	blood
25	chr2:98406400-98469200	Weak transcription	A549	lung
26	chr2:98406800-98416400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:98407400-98422000	Strong transcription	Adipose Nuclei	Adipose
28	chr2:98407400-98422200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:98407800-98422000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:98408200-98415000	Weak transcription	NHEK	skin
31	chr2:98409000-98425000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:98409200-98423600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:98409400-98414600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:98409400-98415000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:98409400-98417000	Weak transcription	Lung	lung
36	chr2:98409400-98418600	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:98409400-98423400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:98409400-98423600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:98409400-98423600	Weak transcription	Psoas Muscle	Psoas
40	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
41	chr2:98409600-98415000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:98409600-98415600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:98409600-98418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:98409600-98419800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:98409600-98429800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:98409800-98425000	Weak transcription	Fetal Brain Female	brain
47	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
48	chr2:98410000-98414600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:98410000-98415000	Weak transcription	Fetal Thymus	thymus
50	chr2:98410000-98415000	Weak transcription	Ovary	ovary

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