Variant report

Variant	rs6723466
Chromosome Location	chr2:98485416-98485417
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98481137..98483396-chr2:98485163..98486842,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10176201	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10182941	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200949	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10211231	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1071885	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865055	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11123924	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123949	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123966	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11690482	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11693874	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11888323	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11899171	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712123	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12712174	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13003978	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13006817	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13008503	0.88[ASN][1000 genomes]
rs13010946	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13022778	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13034644	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1317178	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13405546	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466020	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1466924	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503200	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1922280	0.97[ASN][1000 genomes]
rs1922282	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017028	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2091772	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2100058	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2141862	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279825	0.85[ASN][1000 genomes]
rs2279826	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2305142	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2309316	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309317	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2309356	0.89[ASN][1000 genomes]
rs3088327	0.80[ASN][1000 genomes]
rs3762593	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4274643	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4560167	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5865	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6543108	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6543109	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6543161	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543177	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543202	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6543210	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6707924	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6709571	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710813	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6719556	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6723653	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6744331	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6748809	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6748927	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7558931	0.89[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes]
rs7561104	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562695	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7567397	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7574437	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7577886	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7582664	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7586210	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[ASN][1000 genomes]
rs7598116	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7602412	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7605180	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs930607	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9308862	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs956696	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9973416	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6723466	ZAP70	cis	Nerve Tibial	GTEx
rs6723466	TMEM131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98434400-98485800	Weak transcription	Lung	lung
2	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:98457000-98485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:98457200-98485800	Weak transcription	Brain Anterior Caudate	brain
5	chr2:98457400-98485800	Weak transcription	Aorta	Aorta
6	chr2:98458200-98486000	Weak transcription	Ovary	ovary
7	chr2:98458200-98486800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:98458600-98485600	Weak transcription	Placenta	Placenta
9	chr2:98460000-98486000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:98462800-98485600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:98466600-98485600	Weak transcription	Brain Angular Gyrus	brain
12	chr2:98467000-98486800	Weak transcription	K562	blood
13	chr2:98468400-98486400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:98468600-98486200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:98469200-98486000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:98469400-98486600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:98471400-98485800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:98475400-98485800	Weak transcription	Gastric	stomach
19	chr2:98475600-98485600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:98475800-98485600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:98475800-98486600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:98476200-98486800	Weak transcription	Small Intestine	intestine
23	chr2:98476600-98486000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:98476800-98486800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:98478400-98485600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:98478600-98485600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:98478600-98485800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:98478600-98485800	Weak transcription	Liver	Liver
29	chr2:98478600-98485800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:98478600-98485800	Weak transcription	Esophagus	oesophagus
31	chr2:98478600-98485800	Weak transcription	Fetal Stomach	stomach
32	chr2:98478600-98486200	Weak transcription	Fetal Lung	lung
33	chr2:98478600-98502200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:98478600-98502800	Weak transcription	Colonic Mucosa	Colon
35	chr2:98478600-98502800	Weak transcription	Pancreas	Pancrea
36	chr2:98478800-98485800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:98478800-98486800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:98478800-98489800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:98481600-98485600	Weak transcription	GM12878-XiMat	blood
40	chr2:98482400-98486000	Weak transcription	Primary T cells from cord blood	blood
41	chr2:98483600-98486000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:98483800-98487600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:98484000-98485600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:98484000-98485600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:98484000-98485600	Enhancers	HMEC	breast
46	chr2:98484000-98485800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:98484000-98486000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:98484000-98486200	Enhancers	Psoas Muscle	Psoas
49	chr2:98484000-98487200	Enhancers	Left Ventricle	heart
50	chr2:98484000-98487800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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