Variant report

Variant	rs6703653
Chromosome Location	chr1:84555908-84555909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84541438..84545739-chr1:84555567..84558104,4	K562	blood:
2	chr1:84553847..84557736-chr1:84560723..84565476,4	K562	blood:
3	chr1:84551652..84556823-chr1:84558383..84561144,5	K562	blood:
4	chr1:84549201..84550901-chr1:84554947..84556654,2	K562	blood:
5	chr1:84554743..84559247-chr1:84561300..84565476,7	K562	blood:

Variant related genes	Relation type
ENSG00000271576	Chromatin interaction
ENSG00000142875	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1021491	0.89[AMR][1000 genomes]
rs10493750	0.90[JPT][hapmap]
rs10782822	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10874427	0.84[MEX][hapmap]
rs11163897	0.84[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11163898	0.89[JPT][hapmap]
rs11163900	0.90[JPT][hapmap]
rs12132032	0.89[JPT][hapmap]
rs12404263	0.84[JPT][hapmap]
rs12405120	0.90[JPT][hapmap]
rs12724598	0.90[JPT][hapmap]
rs12746741	0.82[JPT][hapmap]
rs2250806	0.84[ASW][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs2792973	0.88[AMR][1000 genomes]
rs2792975	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs2792976	0.86[AMR][1000 genomes]
rs3861699	0.84[JPT][hapmap]
rs4907193	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674038	0.84[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6701486	0.81[GIH][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes]
rs7520283	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];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]
rs957828	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6703653	MCOLN2	cis	parietal	SCAN
rs6703653	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84544600-84556200	Weak transcription	Pancreas	Pancrea
2	chr1:84544600-84557200	Weak transcription	Gastric	stomach
3	chr1:84544800-84556000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:84544800-84556200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:84545000-84556200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:84545000-84557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:84545000-84558800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:84545000-84560600	Weak transcription	Fetal Lung	lung
9	chr1:84545000-84561200	Weak transcription	Ovary	ovary
10	chr1:84545000-84566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:84545000-84570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:84545200-84568600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:84545400-84556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:84545400-84560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:84545800-84568600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:84546400-84560400	Weak transcription	Dnd41	blood
17	chr1:84552200-84556000	Weak transcription	Spleen	Spleen
18	chr1:84552200-84556200	Weak transcription	Left Ventricle	heart
19	chr1:84552200-84556200	Weak transcription	Right Ventricle	heart
20	chr1:84552200-84558600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:84552200-84561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:84552200-84561800	Weak transcription	Right Atrium	heart
23	chr1:84552200-84569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:84552400-84557200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:84552600-84562000	Weak transcription	Fetal Stomach	stomach
26	chr1:84553600-84556200	Enhancers	Fetal Heart	heart
27	chr1:84554200-84556400	Enhancers	Brain Hippocampus Middle	brain
28	chr1:84554200-84556400	Enhancers	HSMM	muscle
29	chr1:84554400-84556200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:84554400-84556400	Enhancers	A549	lung
31	chr1:84554400-84556600	Enhancers	Hela-S3	cervix
32	chr1:84554400-84556600	Enhancers	HMEC	breast
33	chr1:84554600-84556000	Enhancers	Brain Substantia Nigra	brain
34	chr1:84554600-84556400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:84554600-84556400	Enhancers	HUVEC	blood vessel
36	chr1:84554600-84556600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:84554600-84556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:84554600-84556800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:84554600-84560000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:84554800-84556400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:84554800-84556400	Enhancers	NHDF-Ad	bronchial
42	chr1:84554800-84556600	Enhancers	NHEK	skin
43	chr1:84554800-84556600	Enhancers	NHLF	lung
44	chr1:84554800-84556600	Enhancers	Osteobl	bone
45	chr1:84555000-84556400	Enhancers	K562	blood
46	chr1:84555000-84556800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr1:84555000-84557000	Enhancers	Fetal Intestine Small	intestine
48	chr1:84555000-84557200	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr1:84555200-84556000	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:84555200-84556200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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