Variant report

Variant	rs2270013
Chromosome Location	chr22:31042352-31042353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31031427..31034131-chr22:31040596..31042589,2	K562	blood:
2	chr22:31037150..31040336-chr22:31042164..31045603,3	K562	blood:
3	chr22:31039922..31042444-chr22:31043660..31045429,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100036	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005887	0.86[CHB][hapmap]
rs10439913	0.82[AMR][1000 genomes]
rs1076301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs11089468	0.89[ASN][1000 genomes]
rs12159167	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13056901	0.90[AMR][1000 genomes]
rs1801198	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1971653	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1981590	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1981591	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072194	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2078976	0.86[ASN][1000 genomes]
rs2240002	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2267163	0.87[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2267164	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3179442	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3887855	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4375972	0.83[EUR][1000 genomes]
rs4513384	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820023	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5019308	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749141	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749144	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749147	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749149	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753236	0.84[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs5753250	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753252	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5753259	0.85[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753265	0.86[ASN][1000 genomes]
rs5994328	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997704	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes]
rs5997711	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997714	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997715	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713853	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs757027	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs8138932	0.88[EUR][1000 genomes]
rs8139950	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2270013	GAL3ST1	cis	cerebellum	SCAN
rs2270013	DUSP18	cis	lymphoblastoid	seeQTL
rs2270013	MORC2	cis	cerebellum	SCAN
rs2270013	PES1	cis	parietal	SCAN
rs2270013	LIF	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31032400-31052400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:31032800-31046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31033200-31052000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr22:31033400-31058200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr22:31033600-31058000	Weak transcription	Adipose Nuclei	Adipose
6	chr22:31033600-31058000	Weak transcription	Fetal Lung	lung
7	chr22:31033800-31042600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr22:31033800-31046600	Weak transcription	Fetal Intestine Small	intestine
9	chr22:31033800-31057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:31034000-31042400	Weak transcription	Brain Germinal Matrix	brain
11	chr22:31034000-31043000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr22:31034000-31045000	Weak transcription	HUVEC	blood vessel
13	chr22:31034000-31045000	Weak transcription	NHEK	skin
14	chr22:31034000-31045200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr22:31034000-31045400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr22:31034000-31046400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr22:31034000-31049800	Weak transcription	Fetal Brain Female	brain
18	chr22:31034000-31059400	Weak transcription	Aorta	Aorta
19	chr22:31034200-31045600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr22:31034200-31057800	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:31034200-31058800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr22:31037200-31042800	Weak transcription	Fetal Stomach	stomach
23	chr22:31037200-31045000	Weak transcription	Colonic Mucosa	Colon
24	chr22:31037200-31045400	Weak transcription	Lung	lung
25	chr22:31037400-31042400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr22:31037400-31042600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr22:31039400-31050600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr22:31039800-31042400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:31039800-31042600	Weak transcription	Pancreas	Pancrea
30	chr22:31039800-31043400	Weak transcription	Ovary	ovary
31	chr22:31039800-31045600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr22:31039800-31046600	Weak transcription	Right Atrium	heart
33	chr22:31040000-31042400	Weak transcription	Gastric	stomach
34	chr22:31040000-31042400	Weak transcription	Spleen	Spleen
35	chr22:31040000-31042600	Weak transcription	Right Ventricle	heart
36	chr22:31040000-31045200	Weak transcription	Esophagus	oesophagus
37	chr22:31040000-31045200	Weak transcription	GM12878-XiMat	blood
38	chr22:31040200-31045000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr22:31040200-31045000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr22:31040200-31045600	Weak transcription	Left Ventricle	heart
41	chr22:31040200-31046400	Weak transcription	Fetal Muscle Leg	muscle
42	chr22:31040200-31046600	Weak transcription	Psoas Muscle	Psoas
43	chr22:31040200-31060800	Weak transcription	Fetal Brain Male	brain
44	chr22:31040400-31042400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr22:31040400-31044800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr22:31040600-31042600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr22:31040600-31043600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr22:31040600-31045000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr22:31040600-31045000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr22:31040600-31045000	Weak transcription	HSMM	muscle

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