Variant report

Variant	rs877187
Chromosome Location	chr6:33706211-33706212
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	chr6:33704352..33707039-chr6:33718768..33721610,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10456075	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs10456420	0.85[EUR][1000 genomes]
rs10947432	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947441	1.00[LWK][hapmap];0.90[MKK][hapmap]
rs11757379	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12153877	0.84[EUR][1000 genomes]
rs12189725	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];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190155	0.85[ASN][1000 genomes]
rs12192035	0.89[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193658	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12195409	0.85[EUR][1000 genomes]
rs12198383	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12199132	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203688	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204620	0.85[EUR][1000 genomes]
rs12204992	0.85[EUR][1000 genomes]
rs12205398	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12211490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211554	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211565	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214669	1.00[LWK][hapmap]
rs12215329	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660955	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12661400	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662447	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13200063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13203745	1.00[LWK][hapmap];0.90[MKK][hapmap]
rs13204162	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13204975	0.85[ASN][1000 genomes]
rs13206228	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13207666	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213889	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13214874	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2274459	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281831	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281917	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2281918	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs2281919	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs2296737	0.82[ASN][1000 genomes]
rs2296749	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34139049	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34339105	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34460651	0.86[EUR][1000 genomes]
rs34472165	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34869648	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34884883	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35274562	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35366046	0.81[EUR][1000 genomes]
rs35445446	0.93[EUR][1000 genomes]
rs35646598	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35698850	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35721478	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35797388	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36122085	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3793080	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs3806107	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs3818526	0.85[ASN][1000 genomes]
rs3818532	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs4559081	1.00[LWK][hapmap]
rs66617522	0.80[EUR][1000 genomes]
rs66670017	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68168863	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925337	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs729376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751095	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs755239	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296097	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.82[ASN][1000 genomes]
rs9469554	0.82[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap]

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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs877187	ITPR3	cis	multi-tissue	Pritchard
rs877187	C6orf125	cis	cerebellum	SCAN
rs877187	LEMD2	cis	cerebellum	SCAN
rs877187	LEMD2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:33690800-33708200	Weak transcription	Gastric	stomach
3	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:33692000-33706800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:33699200-33710000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:33699800-33708000	Weak transcription	Fetal Lung	lung
11	chr6:33700200-33706600	Weak transcription	Fetal Intestine Large	intestine
12	chr6:33700400-33707400	Weak transcription	Lung	lung
13	chr6:33700600-33707200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:33702000-33710000	Genic enhancers	HSMM	muscle
15	chr6:33703400-33706800	Weak transcription	Spleen	Spleen
16	chr6:33704400-33707800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr6:33704600-33706600	Genic enhancers	Brain Substantia Nigra	brain
18	chr6:33704800-33706400	Enhancers	Fetal Heart	heart
19	chr6:33704800-33706800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:33704800-33707000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:33705000-33706400	Enhancers	Pancreas	Pancrea
22	chr6:33705200-33707200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:33705200-33709800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:33705400-33707000	Genic enhancers	Left Ventricle	heart
25	chr6:33705400-33708000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:33705400-33709000	Enhancers	Liver	Liver
27	chr6:33705400-33712000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:33705600-33706800	Weak transcription	Right Atrium	heart
29	chr6:33705600-33707600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:33705600-33707600	Weak transcription	Placenta	Placenta
31	chr6:33705600-33707600	Weak transcription	HSMMtube	muscle
32	chr6:33705600-33708000	Weak transcription	Brain Angular Gyrus	brain
33	chr6:33705600-33709200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
34	chr6:33705800-33706800	Genic enhancers	Psoas Muscle	Psoas
35	chr6:33705800-33707800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:33705800-33711000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:33706000-33706800	Enhancers	Colonic Mucosa	Colon
38	chr6:33706000-33706800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr6:33706200-33706600	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:33706200-33707000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:33706200-33707400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:33706200-33707400	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:33706200-33707800	Genic enhancers	Right Ventricle	heart
44	chr6:33706200-33707800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle

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