Variant report

Variant	rs1878898
Chromosome Location	chr2:86121484-86121485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86114878..86116961-chr2:86120705..86124277,3	MCF-7	breast:
2	chr2:86115047..86116757-chr2:86119715..86122326,2	MCF-7	breast:
3	chr2:86119682..86121677-chr2:86130359..86133618,3	MCF-7	breast:
4	chr2:86119817..86123713-chr2:86130856..86134451,3	K562	blood:

Variant related genes	Relation type
ENSG00000272564	Chromatin interaction
ENSG00000115525	Chromatin interaction
ENSG00000232504	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10496320	0.84[JPT][hapmap]
rs11127006	0.84[JPT][hapmap]
rs1135603	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12614498	0.82[CHB][hapmap]
rs12622987	0.84[JPT][hapmap]
rs13008291	0.93[ASN][1000 genomes]
rs13014421	0.84[JPT][hapmap]
rs1401384	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1518983	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1518991	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543972	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026675	0.83[JPT][hapmap]
rs17026750	0.91[CEU][hapmap]
rs1878899	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1878904	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577770	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577771	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577772	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2577774	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577775	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577777	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577778	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577779	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577780	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577786	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2679710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2679711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2679712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679714	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679715	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679716	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2679717	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679718	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679719	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2679720	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2679721	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2679722	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs2679725	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28364794	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918014	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918015	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918016	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2945823	0.87[EUR][1000 genomes]
rs2945825	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2945826	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35153287	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3810821	0.84[JPT][hapmap]
rs4832016	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4832210	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4832216	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4832217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62150576	0.94[ASN][1000 genomes]
rs6547636	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap]
rs6720161	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap]
rs6734115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6735629	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];1.00[ASN][1000 genomes]
rs6747179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6747294	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750686	0.87[CEU][hapmap]
rs7572209	0.84[JPT][hapmap]
rs7593080	0.80[EUR][1000 genomes]
rs764471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs954176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959313	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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1878898	ST3GAL5	cis	cerebellum	SCAN
rs1878898	IMMT	cis	cerebellum	SCAN
rs1878898	PTCD3	cis	cerebellum	SCAN
rs1878898	C2orf51	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86117400-86126400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:86118000-86121600	Enhancers	Fetal Muscle Leg	muscle
3	chr2:86118200-86122200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:86118200-86126000	Weak transcription	Primary T cells from cord blood	blood
5	chr2:86118200-86126800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:86118400-86126600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:86118400-86127600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:86118600-86131000	Weak transcription	Thymus	Thymus
9	chr2:86118800-86121600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:86118800-86122400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:86119200-86121600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:86119200-86122000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:86119400-86121600	Enhancers	Dnd41	blood
14	chr2:86119400-86122000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:86119400-86122200	Enhancers	HMEC	breast
16	chr2:86119600-86121600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:86119600-86121600	Enhancers	Adipose Nuclei	Adipose
18	chr2:86119600-86121800	Enhancers	HSMM	muscle
19	chr2:86119600-86122000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:86119600-86122000	Flanking Active TSS	A549	lung
21	chr2:86119800-86121800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:86119800-86121800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:86119800-86122000	Enhancers	Osteobl	bone
24	chr2:86119800-86132200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:86120000-86126600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:86120200-86122000	Enhancers	NHDF-Ad	bronchial
27	chr2:86120200-86134200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:86120400-86121800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:86120600-86121600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:86120600-86121600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:86120600-86121600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:86120600-86121600	Enhancers	HSMMtube	muscle
33	chr2:86120600-86121600	Enhancers	HUVEC	blood vessel
34	chr2:86120600-86121800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:86120600-86121800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:86120600-86121800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:86120800-86121600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:86120800-86131400	Weak transcription	Pancreas	Pancrea
39	chr2:86121000-86122000	Enhancers	Brain Anterior Caudate	brain
40	chr2:86121000-86122600	Enhancers	NHEK	skin
41	chr2:86121200-86121600	Enhancers	Brain Angular Gyrus	brain
42	chr2:86121200-86121600	Flanking Active TSS	NH-A	brain
43	chr2:86121200-86123800	Weak transcription	Lung	lung
44	chr2:86121200-86126600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:86121400-86121600	Enhancers	Brain Hippocampus Middle	brain
46	chr2:86121400-86121800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:86121400-86121800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:86121400-86121800	Enhancers	Brain Cingulate Gyrus	brain
49	chr2:86121400-86121800	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr2:86121400-86122200	Enhancers	Muscle Satellite Cultured Cells	--

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