Variant report

Variant	rs2017028
Chromosome Location	chr2:98589451-98589452
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	chr2:98586492..98590623-chr2:98609849..98613256,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10176201	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10200949	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10211231	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1071885	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123924	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11123949	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123966	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11690482	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11693874	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888323	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899171	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12712123	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13003978	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006817	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022778	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs13405546	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1466924	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1503200	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1922280	0.86[ASN][1000 genomes]
rs1922282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2100058	0.80[ASN][1000 genomes]
rs2141862	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279825	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309316	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs2309317	0.85[AFR][1000 genomes]
rs2309356	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088327	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762593	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4560167	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6543109	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6543161	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6543177	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6543202	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6543210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707924	0.82[AFR][1000 genomes]
rs6709571	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719556	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6723466	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6723653	0.88[ASN][1000 genomes]
rs6744331	0.85[ASN][1000 genomes]
rs6748809	0.84[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs6748927	0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs7561104	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7562695	0.84[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7574437	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7577886	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7582664	0.84[ASN][1000 genomes]
rs7586210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598116	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602412	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605180	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308862	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs956696	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9973416	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv3451267	chr2:98588690-98590336	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2017028	CNNM3	cis	cerebellum	SCAN
rs2017028	ZAP70	cis	Nerve Tibial	GTEx
rs2017028	ADRA2B	cis	cerebellum	SCAN
rs2017028	ZAP70	cis	cerebellum	SCAN
rs2017028	FAM178B	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:98575400-98595000	Weak transcription	HSMM	muscle
5	chr2:98580000-98589800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:98581000-98589600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:98583600-98595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:98584600-98590000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:98584600-98597000	Weak transcription	Thymus	Thymus
10	chr2:98585000-98608400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:98585200-98589800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:98585400-98591200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:98585600-98594800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:98586600-98589600	Weak transcription	Fetal Lung	lung
15	chr2:98586800-98590600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:98587000-98594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:98587000-98595600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:98587200-98589800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:98587200-98589800	Weak transcription	Right Atrium	heart
20	chr2:98587200-98590000	Weak transcription	Primary T cells from cord blood	blood
21	chr2:98587200-98591200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr2:98587400-98589800	Weak transcription	Left Ventricle	heart
23	chr2:98587400-98592400	Weak transcription	Ovary	ovary
24	chr2:98587400-98599600	Weak transcription	Spleen	Spleen
25	chr2:98587800-98595400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:98587800-98600000	Weak transcription	Gastric	stomach
27	chr2:98588000-98589600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:98588200-98592600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr2:98588200-98596000	Weak transcription	Stomach Mucosa	stomach
30	chr2:98588400-98589600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:98588400-98590200	Enhancers	Psoas Muscle	Psoas
32	chr2:98588600-98590400	Weak transcription	Pancreas	Pancrea
33	chr2:98588600-98598200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:98589000-98590200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:98589000-98590400	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr2:98589000-98590600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
37	chr2:98589200-98589600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:98589200-98590000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:98589200-98590000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:98589200-98590200	ZNF genes & repeats	GM12878-XiMat	blood
41	chr2:98589200-98591600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr2:98589200-98597400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:98589400-98590000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:98589400-98592000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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