Variant report

Variant	rs6547673
Chromosome Location	chr2:86528938-86528939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86528161..86530065-chr2:86667250..86669101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1007502	0.90[JPT][hapmap]
rs10165626	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10186289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10189492	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10200186	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10200526	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10200619	0.84[CHB][hapmap]
rs10204589	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs10520415	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11127019	0.81[JPT][hapmap]
rs11127024	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11127026	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11127028	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11676515	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11680025	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11685863	0.84[CHB][hapmap]
rs11687392	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs11689971	0.81[JPT][hapmap]
rs12469233	0.83[AMR][1000 genomes]
rs12472390	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12472676	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12478575	0.86[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12478653	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12620833	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12622200	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12714179	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12714180	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12999029	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13000103	0.85[JPT][hapmap]
rs13005014	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs13017143	0.81[CEU][hapmap]
rs13017338	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13020869	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13023154	0.85[CEU][hapmap]
rs13024436	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs13024964	0.82[CEU][hapmap]
rs13421310	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1559514	0.95[JPT][hapmap]
rs17738058	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17738096	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1863050	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1863051	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs1863052	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs1863056	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1863057	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1863058	0.85[JPT][hapmap]
rs1863060	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1863061	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1863063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042502	0.95[JPT][hapmap]
rs2113615	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2276625	0.85[JPT][hapmap]
rs2278105	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs2367232	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs28488524	0.80[ASN][1000 genomes]
rs34048420	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34069316	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35160687	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35281683	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35370705	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35762338	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4610056	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4832036	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs4832263	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4832265	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4832271	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4832274	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4832276	0.85[JPT][hapmap]
rs6713456	0.86[CEU][hapmap];0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6714362	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6728029	0.96[ASN][1000 genomes]
rs67407963	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6746198	0.84[CHB][hapmap]
rs6758173	1.00[JPT][hapmap]
rs67903513	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs718292	0.85[JPT][hapmap]
rs7563887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569654	0.81[JPT][hapmap]
rs7571424	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7593440	0.84[CHB][hapmap]
rs9309635	0.80[CHB][hapmap];0.86[JPT][hapmap]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6547673	IMMT	cis	Nerve Tibial	GTEx
rs6547673	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs6547673	IMMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86514000-86529200	Weak transcription	Pancreas	Pancrea
2	chr2:86522600-86529000	Weak transcription	Small Intestine	intestine
3	chr2:86524000-86529600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr2:86524200-86530000	Enhancers	Brain Hippocampus Middle	brain
5	chr2:86524200-86530200	Enhancers	Colon Smooth Muscle	Colon
6	chr2:86524200-86533600	Enhancers	Fetal Lung	lung
7	chr2:86524600-86533400	Enhancers	Fetal Muscle Leg	muscle
8	chr2:86524800-86530200	Enhancers	Brain Angular Gyrus	brain
9	chr2:86525000-86529200	Enhancers	Fetal Muscle Trunk	muscle
10	chr2:86525000-86530200	Enhancers	HSMMtube	muscle
11	chr2:86525200-86529600	Enhancers	Brain Anterior Caudate	brain
12	chr2:86525200-86530200	Enhancers	Brain Germinal Matrix	brain
13	chr2:86525600-86529600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:86525600-86530200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:86525800-86530000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:86525800-86530200	Enhancers	Fetal Brain Female	brain
17	chr2:86525800-86540800	Weak transcription	Aorta	Aorta
18	chr2:86526200-86529600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:86526400-86529200	Weak transcription	Esophagus	oesophagus
20	chr2:86526400-86529600	Enhancers	Brain Substantia Nigra	brain
21	chr2:86526400-86529800	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:86526400-86530000	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:86526400-86530200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:86526600-86529000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:86526600-86529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:86526800-86529400	Weak transcription	Fetal Heart	heart
27	chr2:86527000-86529400	Enhancers	Ovary	ovary
28	chr2:86527000-86530200	Enhancers	Fetal Stomach	stomach
29	chr2:86527200-86529600	Enhancers	Left Ventricle	heart
30	chr2:86527400-86529400	Enhancers	Fetal Brain Male	brain
31	chr2:86527400-86529600	Enhancers	Right Atrium	heart
32	chr2:86527400-86530000	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:86527600-86529600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:86527800-86529000	Weak transcription	Right Ventricle	heart
35	chr2:86528000-86529800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:86528000-86530000	Enhancers	HSMM	muscle
37	chr2:86528200-86529200	Weak transcription	Spleen	Spleen
38	chr2:86528200-86529400	Enhancers	Lung	lung
39	chr2:86528400-86529400	Enhancers	Psoas Muscle	Psoas
40	chr2:86528600-86529800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:86528600-86530000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr2:86528800-86529000	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:86528800-86529200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:86528800-86529200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:86528800-86529200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:86528800-86529400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:86528800-86529400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:86528800-86529400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:86528800-86529400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
50	chr2:86528800-86529600	Enhancers	Fetal Intestine Large	intestine

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