Variant report

Variant	rs2280256
Chromosome Location	chr2:99449174-99449175
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	chr2:99345811..99349934-chr2:99448435..99450285,3	MCF-7	breast:
2	chr2:99443633..99446031-chr2:99448768..99450507,2	K562	blood:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10169003	0.86[EUR][1000 genomes]
rs10172158	0.83[EUR][1000 genomes]
rs10181972	0.86[EUR][1000 genomes]
rs10188156	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11123755	0.83[EUR][1000 genomes]
rs11887536	0.83[EUR][1000 genomes]
rs12468024	0.83[EUR][1000 genomes]
rs12712033	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12712035	0.90[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712036	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs12712038	0.83[EUR][1000 genomes]
rs12712039	0.82[EUR][1000 genomes]
rs12992214	0.81[AMR][1000 genomes]
rs12999225	0.81[JPT][hapmap]
rs13004923	0.86[EUR][1000 genomes]
rs13389386	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1356424	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1568213	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1581250	0.86[EUR][1000 genomes]
rs1581251	0.83[EUR][1000 genomes]
rs1878585	0.86[EUR][1000 genomes]
rs1983352	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2138082	0.82[EUR][1000 genomes]
rs2276604	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4263159	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4850888	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4851162	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4851163	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851167	0.83[EUR][1000 genomes]
rs4851170	0.83[EUR][1000 genomes]
rs4851171	0.82[EUR][1000 genomes]
rs6542838	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542839	0.84[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs6711022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6713991	0.87[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6714243	0.83[EUR][1000 genomes]
rs6717372	0.81[EUR][1000 genomes]
rs6719634	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs6726156	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6733011	0.84[ASN][1000 genomes]
rs6757099	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7579189	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7581128	0.80[JPT][hapmap]
rs7608889	0.83[EUR][1000 genomes]
rs981601	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs981602	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2280256	FAHD2B	cis	parietal	SCAN
rs2280256	LIPT1	cis	parietal	SCAN
rs2280256	FAM178B	cis	parietal	SCAN
rs2280256	MAL	cis	parietal	SCAN
rs2280256	TSGA10	cis	multi-tissue	Pritchard
rs2280256	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99440200-99449800	Weak transcription	Colonic Mucosa	Colon
3	chr2:99440400-99453800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
5	chr2:99440600-99449600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:99440600-99449600	Weak transcription	HMEC	breast
7	chr2:99440600-99453800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:99441000-99449600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:99442600-99449800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:99443600-99450400	Weak transcription	Pancreas	Pancrea
11	chr2:99443800-99449600	Weak transcription	Gastric	stomach
12	chr2:99444200-99450800	Enhancers	HepG2	liver
13	chr2:99444200-99451000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:99445400-99450000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr2:99445600-99450800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:99446000-99449400	Weak transcription	Spleen	Spleen
17	chr2:99446000-99449800	Weak transcription	Stomach Mucosa	stomach
18	chr2:99446000-99450200	Weak transcription	Right Atrium	heart
19	chr2:99446200-99449400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:99446400-99451600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:99446400-99451600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:99446600-99449600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:99446600-99449800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:99446600-99449800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:99446800-99449400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:99446800-99449800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:99446800-99452000	Weak transcription	Primary T cells from cord blood	blood
28	chr2:99447000-99450400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:99447200-99450000	Strong transcription	Fetal Intestine Small	intestine
30	chr2:99447600-99451000	Enhancers	Left Ventricle	heart
31	chr2:99447800-99449200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:99447800-99449400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:99447800-99449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:99448400-99449200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:99448400-99449800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:99448400-99451000	Enhancers	Lung	lung
37	chr2:99448400-99454000	Enhancers	Fetal Thymus	thymus
38	chr2:99448600-99449200	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:99448600-99449600	Strong transcription	Esophagus	oesophagus
40	chr2:99448600-99450600	Enhancers	Fetal Muscle Leg	muscle
41	chr2:99448600-99450800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:99448600-99451000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr2:99448800-99449400	Weak transcription	Brain Angular Gyrus	brain
44	chr2:99448800-99452400	Enhancers	HUVEC	blood vessel
45	chr2:99449000-99449800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:99449000-99450400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:99449000-99450400	Weak transcription	Right Ventricle	heart
48	chr2:99449000-99450600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr2:99449000-99451000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:99449000-99451000	Enhancers	Brain Anterior Caudate	brain

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