Variant report

Variant	rs2842580
Chromosome Location	chr1:185536609-185536610
allele	A/C
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	chr1:185535756-185537087	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:185535769-185536795	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185534952..185537044-chr1:185538888..185541072,3	MCF-7	breast:
2	chr1:185284868..185287511-chr1:185534304..185536690,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228309	TF binding region
ENSG00000116679	Chromatin interaction
ENSG00000273004	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10798024	1.00[JPT][hapmap]
rs11605	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs168004	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs170788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1743273	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs186732	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs193088	0.82[AMR][1000 genomes]
rs2208600	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2756197	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2756199	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2756200	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2756201	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2756203	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2756204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2756205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2756206	0.92[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2756207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2756209	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2821434	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2821435	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2821436	0.95[MEX][hapmap]
rs2821437	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2821438	0.86[EUR][1000 genomes]
rs2842582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842591	0.83[AMR][1000 genomes]
rs333701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs333702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs333703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs333704	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs333705	0.84[AMR][1000 genomes]
rs333708	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs333712	0.80[AMR][1000 genomes]
rs333713	0.80[AMR][1000 genomes]
rs333715	0.90[EUR][1000 genomes]
rs333716	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333717	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333718	0.82[AMR][1000 genomes]
rs333719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333721	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333722	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs333724	0.83[AMR][1000 genomes]
rs333725	0.93[EUR][1000 genomes]
rs333726	0.80[AMR][1000 genomes]
rs333727	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333728	0.83[AMR][1000 genomes]
rs472975	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs479511	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs479559	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs480406	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs488350	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs489418	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs490389	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs491134	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs492436	0.83[AMR][1000 genomes]
rs495416	0.80[AMR][1000 genomes]
rs495791	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs496413	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs498961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs500228	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs503650	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs504627	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs506478	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs507076	0.83[AMR][1000 genomes]
rs509096	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs516040	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs518472	0.80[AMR][1000 genomes]
rs522048	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528985	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529183	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs529275	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs529282	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs530157	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs531472	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs533136	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs534762	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs534920	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs545105	0.81[AMR][1000 genomes]
rs550874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs551806	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs552584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs553280	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs553530	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs554388	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs554711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs558723	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs563215	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs564161	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs564265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs567021	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs567846	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs569496	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs570476	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs571325	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs572252	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs574940	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs579458	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs693523	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs737490	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2842580	FAM129A	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185528600-185539800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:185529400-185543000	Weak transcription	Pancreas	Pancrea
3	chr1:185530800-185544000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:185531800-185540400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:185532800-185538800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:185533000-185538800	Enhancers	HMEC	breast
7	chr1:185533000-185540200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:185533000-185540800	Enhancers	NHEK	skin
9	chr1:185533400-185539000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:185534000-185537000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:185534000-185537200	Enhancers	Fetal Heart	heart
12	chr1:185534200-185537800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:185534200-185540000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:185534400-185538800	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:185534600-185538600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:185534600-185540200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:185534800-185539200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:185534800-185543000	Weak transcription	A549	lung
19	chr1:185535000-185543400	Weak transcription	HSMMtube	muscle
20	chr1:185535200-185538200	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:185535400-185537200	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:185535400-185537200	Enhancers	Small Intestine	intestine
23	chr1:185535800-185536800	Enhancers	Dnd41	blood
24	chr1:185535800-185537000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:185535800-185537200	Enhancers	HUVEC	blood vessel
26	chr1:185535800-185537400	Enhancers	Fetal Intestine Large	intestine
27	chr1:185535800-185537400	Enhancers	Fetal Intestine Small	intestine
28	chr1:185535800-185539000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:185536000-185536800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:185536000-185536800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:185536000-185536800	Enhancers	Fetal Kidney	kidney
32	chr1:185536000-185537000	Enhancers	Stomach Mucosa	stomach
33	chr1:185536000-185537000	Enhancers	NH-A	brain
34	chr1:185536000-185537200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:185536000-185537200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:185536000-185537200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:185536000-185537400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:185536000-185537400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:185536000-185538600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:185536200-185536800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr1:185536200-185537000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:185536200-185537000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:185536200-185537200	Enhancers	Fetal Thymus	thymus
44	chr1:185536200-185537200	Enhancers	Osteobl	bone
45	chr1:185536200-185539000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:185536200-185539400	Enhancers	Primary T cells fromperipheralblood	blood
47	chr1:185536200-185542000	Enhancers	Placenta Amnion	Placenta Amnion
48	chr1:185536400-185536800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:185536400-185536800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:185536400-185536800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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