Variant report

Variant	rs1503200
Chromosome Location	chr2:98578111-98578112
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98572252..98574514-chr2:98576294..98578222,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10176201	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10200949	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10211231	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1071885	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865055	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123924	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11123949	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11123966	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690482	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693874	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11888323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899171	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12712123	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13003978	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006817	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008503	0.83[ASN][1000 genomes]
rs13010946	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13022778	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034644	0.83[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[ASN][1000 genomes]
rs13405546	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1466924	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1922280	0.90[ASN][1000 genomes]
rs1922282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017028	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2091772	0.82[ASN][1000 genomes]
rs2100058	0.84[ASN][1000 genomes]
rs2141862	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279825	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279826	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2309316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2309317	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2309356	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088327	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762593	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4560167	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs5865	0.81[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6543109	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6543161	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543177	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543202	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6543210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707924	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6709571	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6719556	0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6723466	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6723653	0.92[ASN][1000 genomes]
rs6744331	0.89[ASN][1000 genomes]
rs6748809	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6748927	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs7561104	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7562695	0.88[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7574437	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577886	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582664	0.88[ASN][1000 genomes]
rs7586210	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598116	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602412	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930607	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9308862	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs956696	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9973416	0.86[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
rs1503200	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs1503200	ZAP70	cis	Nerve Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:98567600-98586600	Weak transcription	Fetal Stomach	stomach
4	chr2:98568000-98578200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:98568000-98583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:98568200-98580800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:98568400-98586600	Weak transcription	Aorta	Aorta
9	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:98569200-98579400	Weak transcription	Esophagus	oesophagus
11	chr2:98569200-98579600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:98569200-98580600	Weak transcription	NHDF-Ad	bronchial
13	chr2:98569200-98581400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:98571000-98579400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:98571000-98586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:98574000-98578400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:98574200-98580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:98574400-98586200	Weak transcription	NH-A	brain
19	chr2:98574600-98582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:98574600-98583200	Weak transcription	Primary B cells from cord blood	blood
21	chr2:98574600-98583400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:98574800-98579200	Weak transcription	Fetal Heart	heart
23	chr2:98574800-98585200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:98574800-98586200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:98575000-98583000	Weak transcription	Gastric	stomach
26	chr2:98575000-98585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:98575000-98586800	Weak transcription	Brain Angular Gyrus	brain
28	chr2:98575000-98589000	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:98575200-98578200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:98575200-98579000	Weak transcription	NHEK	skin
31	chr2:98575200-98579200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:98575200-98579600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:98575200-98580600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:98575200-98580600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:98575200-98583000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:98575200-98583200	Weak transcription	Small Intestine	intestine
37	chr2:98575200-98584400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:98575400-98579200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:98575400-98579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:98575400-98579400	Weak transcription	Primary T cells from cord blood	blood
42	chr2:98575400-98581400	Weak transcription	Left Ventricle	heart
43	chr2:98575400-98583200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:98575400-98583400	Weak transcription	Spleen	Spleen
45	chr2:98575400-98585000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:98575400-98595000	Weak transcription	HSMM	muscle
47	chr2:98575600-98586600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:98575600-98586600	Weak transcription	Lung	lung
49	chr2:98575800-98579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:98575800-98579400	Weak transcription	Primary B cells from peripheral blood	blood

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