Variant report

Variant	rs5998625
Chromosome Location	chr22:33159872-33159873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32920308-32927723..22:33154607-33167707	H1-hESC	embryonic stem cell:	embryo
2	22:32578360-32590642..22:33154607-33167707	K562	blood:
3	22:32342898-32343477..22:33154607-33167707	Hela-S3	cervix:
4	chr22:33159150..33161467-chr22:33197718..33199220,2	MCF-7	breast:
5	22:32764253-32784733..22:33154607-33167707	K562	blood:
6	22:32053085-32061138..22:33154607-33167707	K562	blood:
7	22:33154607-33167707..22:33262063-33266567	Hela-S3	cervix:
8	22:33154607-33167707..22:33339333-33353583	Hela-S3	cervix:
9	22:32292186-32294405..22:33154607-33167707	K562	blood:
10	22:32594665-32606395..22:33154607-33167707	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000241954	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000254127	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000128253	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000242082	Chromatin interaction
ENSG00000232218	Chromatin interaction
ENSG00000243519	Chromatin interaction
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1018790	0.86[YRI][hapmap]
rs10483165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs1074421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11703138	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs11704261	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs12157546	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12157560	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484506	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484982	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989438	0.82[ASN][1000 genomes]
rs2013544	0.82[ASN][1000 genomes]
rs57852281	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58237391	0.82[ASN][1000 genomes]
rs5994620	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994622	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5998614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998620	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998623	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998624	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998626	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5998627	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5998629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518798	0.82[ASN][1000 genomes]
rs7284103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7286761	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7287602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7287772	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs7289956	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7290713	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7291454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156468	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156471	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156473	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156475	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156480	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156483	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156485	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156486	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156494	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73158303	0.82[ASN][1000 genomes]
rs738990	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs762886	0.82[JPT][hapmap]
rs8135298	0.93[YRI][hapmap]
rs8136169	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8139641	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8142064	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8142758	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9621568	0.82[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5998625	GAL3ST1	cis	parietal	SCAN
rs5998625	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33151000-33175400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:33155000-33161400	Enhancers	Right Atrium	heart
3	chr22:33156200-33160600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:33156200-33161400	Enhancers	Adipose Nuclei	Adipose
5	chr22:33156400-33160200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr22:33156400-33161600	Enhancers	Spleen	Spleen
7	chr22:33157200-33160400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:33157600-33160400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr22:33157600-33160400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:33157800-33160200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr22:33157800-33160200	Weak transcription	Fetal Kidney	kidney
12	chr22:33157800-33160200	Weak transcription	Fetal Lung	lung
13	chr22:33157800-33160400	Weak transcription	NHDF-Ad	bronchial
14	chr22:33158200-33160200	Weak transcription	NHLF	lung
15	chr22:33158200-33160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr22:33158200-33160400	Weak transcription	Esophagus	oesophagus
17	chr22:33158200-33160600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr22:33158400-33160200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr22:33158400-33160200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr22:33158400-33160400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:33158400-33160400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:33158400-33160400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr22:33158400-33160400	Weak transcription	NH-A	brain
24	chr22:33158400-33171800	Weak transcription	HepG2	liver
25	chr22:33158600-33160000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr22:33158800-33160200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:33158800-33160200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:33158800-33160200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr22:33158800-33160200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr22:33158800-33160200	Weak transcription	Osteobl	bone
31	chr22:33158800-33160400	Weak transcription	HSMM	muscle
32	chr22:33158800-33160400	Weak transcription	HSMMtube	muscle
33	chr22:33159200-33160200	Weak transcription	Hela-S3	cervix
34	chr22:33159200-33161800	Enhancers	Placenta	Placenta
35	chr22:33159400-33160400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr22:33159400-33161000	Enhancers	Right Ventricle	heart
37	chr22:33159600-33160400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:33159600-33160400	Enhancers	Stomach Smooth Muscle	stomach
39	chr22:33159600-33160800	Enhancers	Brain Hippocampus Middle	brain
40	chr22:33159600-33161800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr22:33159600-33161800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr22:33159600-33161800	Enhancers	Left Ventricle	heart
43	chr22:33159600-33162000	Enhancers	Fetal Thymus	thymus
44	chr22:33159800-33160400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr22:33159800-33160400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr22:33159800-33161800	Enhancers	Lung	lung
47	chr22:33159800-33162200	Enhancers	Fetal Stomach	stomach

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