Variant report

Variant	rs1878900
Chromosome Location	chr2:86038338-86038339
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	chr2:85963183..85964846-chr2:86037583..86040110,2	MCF-7	breast:
2	chr2:86013750..86016057-chr2:86037086..86038756,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12997305	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13005861	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031939	1.00[ASN][1000 genomes]
rs17431365	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509413	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139202	0.86[EUR][1000 genomes]
rs34593202	1.00[ASN][1000 genomes]
rs34812137	0.88[EUR][1000 genomes]
rs35210068	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35504275	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35699834	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35821122	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909216	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119161	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147505	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72842067	1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1878900	ST3GAL5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86024600-86043600	Weak transcription	Right Ventricle	heart
2	chr2:86028800-86039000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:86029000-86040800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:86029800-86054400	Weak transcription	Spleen	Spleen
5	chr2:86037000-86039200	Enhancers	A549	lung
6	chr2:86037000-86041400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:86037200-86041400	Enhancers	Fetal Lung	lung
8	chr2:86037400-86039600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:86037600-86038600	Enhancers	Fetal Intestine Large	intestine
10	chr2:86037600-86039000	Enhancers	Pancreas	Pancrea
11	chr2:86037600-86039200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:86037600-86039200	Enhancers	Fetal Intestine Small	intestine
13	chr2:86037600-86039200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr2:86037600-86039200	Enhancers	Stomach Mucosa	stomach
15	chr2:86037600-86039600	Enhancers	Lung	lung
16	chr2:86037600-86039600	Enhancers	NH-A	brain
17	chr2:86037600-86039800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:86037600-86039800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:86037600-86039800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:86037600-86039800	Enhancers	Aorta	Aorta
21	chr2:86037600-86039800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr2:86037600-86039800	Enhancers	Right Atrium	heart
23	chr2:86037600-86040600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:86037600-86041400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:86037600-86042600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:86037800-86038400	Enhancers	Fetal Thymus	thymus
27	chr2:86037800-86038400	Enhancers	Osteobl	bone
28	chr2:86037800-86038600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:86037800-86039000	Enhancers	Gastric	stomach
30	chr2:86037800-86039600	Enhancers	HSMM	muscle
31	chr2:86038000-86038400	Flanking Active TSS	Colonic Mucosa	Colon
32	chr2:86038000-86039000	Bivalent Enhancer	Placenta	Placenta
33	chr2:86038000-86039000	Enhancers	Left Ventricle	heart
34	chr2:86038000-86039000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr2:86038000-86039000	Enhancers	HSMMtube	muscle
36	chr2:86038000-86039200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:86038000-86039200	Enhancers	Colon Smooth Muscle	Colon
38	chr2:86038000-86039400	Enhancers	Adipose Nuclei	Adipose
39	chr2:86038000-86039600	Enhancers	Fetal Stomach	stomach
40	chr2:86038000-86039800	Enhancers	Ovary	ovary
41	chr2:86038200-86038400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr2:86038200-86038400	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr2:86038200-86038600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:86038200-86038600	Weak transcription	Liver	Liver
45	chr2:86038200-86038800	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr2:86038200-86039000	Enhancers	Esophagus	oesophagus
47	chr2:86038200-86039000	Enhancers	NHLF	lung
48	chr2:86038200-86039200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:86038200-86039200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr2:86038200-86039400	Enhancers	Fetal Muscle Leg	muscle

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