Variant report

Variant	rs1065314
Chromosome Location	chr22:33258288-33258289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:33257133-33258848	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:33240885-33261662	ProgFib	skin:	n/a	n/a
3	POLR2A	chr22:33258257-33258337	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr22:33257200-33259031	HepG2	liver:	n/a	n/a
5	FOSL2	chr22:33258043-33258901	HepG2	liver:	n/a	n/a
6	POLR2A	chr22:33257996-33258649	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:33254453-33260989	IMR90	lung:	n/a	n/a
8	POLR2A	chr22:33258117-33258826	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32750950-32761732..22:33253287-33262063	Hela-S3	cervix:
2	chr22:33257978..33261996-chr22:33266633..33269916,3	K562	blood:
3	22:32544939-32549151..22:33253287-33262063	Hela-S3	cervix:
4	22:32868055-32872511..22:33253287-33262063	Hela-S3	cervix:
5	22:31961151-31976153..22:33253287-33262063	K562	blood:
6	22:32920308-32927723..22:33253287-33262063	Hela-S3	cervix:
7	chr22:33196558..33199719-chr22:33257750..33262273,4	MCF-7	breast:
8	chr22:33258265..33260703-chr22:33277216..33279656,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000183531	TF binding region
ENSG00000100225	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000100234	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000205856	Chromatin interaction
ENSG00000205853	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1427378	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[AMR][1000 genomes]
rs1427379	0.84[AMR][1000 genomes]
rs1427383	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1427384	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543803	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1543804	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040435	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2040436	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2040437	0.93[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2040438	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2267184	0.93[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28456229	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2899196	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749529	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749532	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5754315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5754322	0.94[MEX][hapmap]
rs80689	0.82[MEX][hapmap]
rs933255	0.94[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9621584	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv3599	chr22:33230106-33274789	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1059368	chr22:33249121-33268782	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1065314	SUGT1P1	trans	parietal	SCAN
rs1065314	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33222600-33258800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr22:33227000-33272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr22:33236200-33259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:33237400-33282200	Weak transcription	Fetal Brain Female	brain
5	chr22:33238400-33259200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:33241600-33258400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:33243400-33260200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr22:33244200-33262000	Weak transcription	Brain Germinal Matrix	brain
9	chr22:33245000-33258800	Weak transcription	Pancreas	Pancrea
10	chr22:33245400-33258800	Strong transcription	HSMM	muscle
11	chr22:33245600-33265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:33245800-33264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:33247000-33258400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr22:33247800-33260200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:33248000-33258400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr22:33249400-33258600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:33249600-33259000	Strong transcription	Fetal Stomach	stomach
18	chr22:33249800-33258800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr22:33249800-33262800	Weak transcription	Brain Angular Gyrus	brain
20	chr22:33250400-33258800	Strong transcription	Osteobl	bone
21	chr22:33250600-33258800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:33250800-33258400	Strong transcription	Spleen	Spleen
23	chr22:33251400-33259000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr22:33251400-33259000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr22:33251400-33259400	Weak transcription	Right Atrium	heart
26	chr22:33251600-33258400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr22:33251600-33258600	Strong transcription	Adipose Nuclei	Adipose
28	chr22:33251600-33259000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:33252400-33259200	Strong transcription	Left Ventricle	heart
30	chr22:33252400-33259200	Weak transcription	Psoas Muscle	Psoas
31	chr22:33252800-33259000	Strong transcription	Fetal Lung	lung
32	chr22:33253000-33258800	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr22:33253200-33258400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr22:33253200-33258400	Strong transcription	Aorta	Aorta
35	chr22:33253200-33258400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr22:33253400-33258800	Strong transcription	HSMMtube	muscle
37	chr22:33254200-33258600	Strong transcription	HMEC	breast
38	chr22:33254400-33258600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr22:33254400-33258800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr22:33254600-33258400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr22:33254600-33258600	Weak transcription	NHEK	skin
42	chr22:33254600-33259400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:33255200-33258400	Weak transcription	Colonic Mucosa	Colon
44	chr22:33255200-33258600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr22:33255200-33263800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr22:33255800-33262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:33256000-33259200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr22:33256000-33262200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr22:33256000-33263800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr22:33256000-33265200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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