Variant report

Variant	rs6547655
Chromosome Location	chr2:86222249-86222250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86179766..86181607-chr2:86220908..86223298,2	K562	blood:
2	chr2:86217426..86219773-chr2:86221522..86225425,4	K562	blood:
3	chr2:86222023..86223749-chr2:86317828..86319791,2	K562	blood:
4	chr2:86221261..86224773-chr2:86231605..86235552,4	K562	blood:
5	chr2:86220130..86224322-chr2:86225400..86228402,3	MCF-7	breast:
6	chr2:86219842..86222798-chr2:86242564..86244317,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10173155	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10186005	0.80[CEU][hapmap]
rs10198260	0.81[AMR][1000 genomes]
rs1020095	0.82[AMR][1000 genomes]
rs10208184	0.88[ASN][1000 genomes]
rs1036553	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127016	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs12714163	0.82[AMR][1000 genomes]
rs12714165	0.82[AMR][1000 genomes]
rs17584697	1.00[CHB][hapmap]
rs2083168	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099616	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099617	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2194486	1.00[CHB][hapmap]
rs2303338	1.00[CHB][hapmap]
rs2886885	0.89[ASN][1000 genomes]
rs311564	0.87[ASN][1000 genomes]
rs311576	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs311578	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs311579	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs311585	0.88[ASN][1000 genomes]
rs311588	0.88[ASN][1000 genomes]
rs3731818	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs3764949	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs3764950	0.95[CHB][hapmap]
rs3821017	0.90[CHB][hapmap]
rs3937593	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4832018	0.82[AMR][1000 genomes]
rs4832020	0.82[AMR][1000 genomes]
rs4832232	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4832233	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6547653	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6547654	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714363	0.82[ASW][hapmap]
rs6731358	1.00[CHB][hapmap]
rs717144	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs7571529	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586985	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7595420	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7599326	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606897	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7607138	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879649	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs893442	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934829	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934831	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs965636	1.00[CHB][hapmap];0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6547655	MRPL35	cis	parietal	SCAN
rs6547655	PTCD3	cis	cerebellum	SCAN
rs6547655	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs6547655	IMMT	cis	cerebellum	SCAN
rs6547655	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs6547655	REEP1	cis	parietal	SCAN
rs6547655	MRPL35	cis	cerebellum	SCAN
rs6547655	IMMT	cis	lymphoblastoid	seeQTL
rs6547655	ST3GAL5	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86207000-86223400	Weak transcription	Liver	Liver
2	chr2:86216000-86222600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:86216000-86223400	Weak transcription	Fetal Lung	lung
4	chr2:86216200-86222800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:86216200-86225800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:86216400-86223200	Weak transcription	Pancreas	Pancrea
7	chr2:86216400-86223400	Weak transcription	Fetal Stomach	stomach
8	chr2:86218400-86223000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:86219800-86224600	Enhancers	Adipose Nuclei	Adipose
10	chr2:86219800-86226400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:86219800-86228600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:86219800-86228800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:86219800-86229000	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:86219800-86229200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:86220000-86223800	Weak transcription	Esophagus	oesophagus
16	chr2:86220400-86223000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:86220400-86227600	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:86220400-86228800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr2:86220800-86223000	Enhancers	Duodenum Mucosa	Duodenum
20	chr2:86220800-86227000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:86220800-86227600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:86220800-86228600	Enhancers	Fetal Muscle Leg	muscle
23	chr2:86220800-86228800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr2:86220800-86228800	Enhancers	Fetal Thymus	thymus
25	chr2:86221000-86222400	Enhancers	Fetal Intestine Small	intestine
26	chr2:86221000-86222400	Enhancers	Left Ventricle	heart
27	chr2:86221000-86222400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:86221000-86222800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:86221000-86222800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:86221000-86223000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:86221000-86223600	Enhancers	Colon Smooth Muscle	Colon
32	chr2:86221000-86224600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:86221000-86224800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:86221000-86225000	Enhancers	Right Ventricle	heart
35	chr2:86221000-86225600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:86221000-86225800	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr2:86221000-86226000	Enhancers	Fetal Heart	heart
38	chr2:86221000-86226400	Enhancers	Colonic Mucosa	Colon
39	chr2:86221000-86227400	Enhancers	Lung	lung
40	chr2:86221000-86228400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:86221000-86228600	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:86221000-86228600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:86221000-86228600	Enhancers	Spleen	Spleen
44	chr2:86221200-86222600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:86221200-86222600	Enhancers	Stomach Smooth Muscle	stomach
46	chr2:86221200-86225800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:86221400-86223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:86221400-86223800	Weak transcription	NHLF	lung
49	chr2:86221400-86227600	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:86221400-86228400	Enhancers	Brain Hippocampus Middle	brain

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