Variant report

Variant	rs2858750
Chromosome Location	chr22:32348239-32348240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:32348180-32348330	BE2_C	brain:	n/a	n/a
2	POLR2A	chr22:32347722-32348350	HepG2	liver:	n/a	n/a
3	CTCF	chr22:32348192-32348321	K562	blood:	n/a	n/a
4	CTCF	chr22:32348120-32348270	HMF	breast:	n/a	n/a
5	CTCF	chr22:32348180-32348330	HEK293	kidney:	n/a	n/a
6	CTCF	chr22:32348120-32348270	HVMF	connective:	n/a	n/a
7	CTCF	chr22:32348180-32348330	HCT-116	colon:	n/a	n/a
8	CTCF	chr22:32348140-32348290	GM06990	blood:	n/a	n/a
9	CTCF	chr22:32348180-32348330	SAEC	small airway:	n/a	n/a
10	RAD21	chr22:32348042-32348386	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr22:32348140-32348290	HRE	kidney:	n/a	n/a
12	CTCF	chr22:32348185-32348273	GM19238	blood:	n/a	n/a
13	CTCF	chr22:32348100-32348250	HA-sp	spinal cord:	n/a	n/a
14	CTCF	chr22:32348140-32348290	HCM	heart:	n/a	n/a
15	CTCF	chr22:32348140-32348290	AG10803	skin:	n/a	n/a
16	CTCF	chr22:32348120-32348270	GM12864	blood:	n/a	n/a
17	RAD21	chr22:32348149-32348947	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr22:32348160-32348310	NHLF	lung:	n/a	n/a
19	CTCF	chr22:32348172-32348315	GM12878	blood:	n/a	n/a
20	CTCF	chr22:32348220-32348299	Pancreas_OC	pancreas:	n/a	n/a
21	CTCF	chr22:32348180-32348330	MCF-7	breast:	n/a	n/a
22	CTCF	chr22:32348100-32348250	AG09309	skin:	n/a	n/a
23	CTCF	chr22:32348180-32348330	HRPEpiC	eye:	n/a	n/a
24	RAD21	chr22:32348036-32348375	HepG2	liver:	n/a	n/a
25	POLR2A	chr22:32345555-32348344	K562	blood:	n/a	n/a
26	CTCF	chr22:32348160-32348310	HEK293	kidney:	n/a	n/a
27	WRNIP1	chr22:32348216-32348270	GM12878	blood:	n/a	n/a
28	CTCF	chr22:32348180-32348330	AG04450	lung:	n/a	n/a
29	POLR2A	chr22:32347708-32348299	HL-60	blood:	n/a	n/a
30	POLR2A	chr22:32347668-32348284	MCF-7	breast:	n/a	n/a
31	POLR2A	chr22:32347672-32348343	GM12892	blood:	n/a	n/a
32	CTCF	chr22:32348183-32348275	GM12892	blood:	n/a	n/a
33	POLR2A	chr22:32348028-32349183	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr22:32348180-32348330	GM12873	blood:	n/a	n/a
35	CEBPB	chr22:32347950-32349028	Hela-S3	cervix:	n/a	n/a
36	RAD21	chr22:32347919-32348574	SK-N-SH	brain:	n/a	n/a
37	CTCF	chr22:32348140-32348290	HPF	lung:	n/a	n/a
38	SMC3	chr22:32347901-32348509	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr22:32347773-32348344	K562	blood:	n/a	n/a
40	CTCF	chr22:32348140-32348330	HepG2	liver:	n/a	n/a
41	CTCF	chr22:32348160-32348310	Caco-2	colon:	n/a	n/a
42	CTCF	chr22:32348180-32348330	WERI-Rb-1	eye:	n/a	n/a
43	CTCF	chr22:32348120-32348270	BJ	skin:	n/a	n/a
44	CTCF	chr22:32348140-32348290	GM12873	blood:	n/a	n/a
45	MAX	chr22:32348085-32348363	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr22:32348160-32348310	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr22:32348200-32348350	NB4	blood:	n/a	n/a
48	CTCF	chr22:32348200-32348350	HMEC	breast:	n/a	n/a
49	CTCF	chr22:32348140-32348290	HepG2	liver:	n/a	n/a
50	CTCF	chr22:32348172-32348327	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32053085-32061138..22:32347255-32351014	GM12878	blood:
2	chr22:32264603..32274220-chr22:32339477..32348693,21	K562	blood:
3	22:32170492-32188129..22:32347255-32351014	K562	blood:
4	22:32012966-32043914..22:32347255-32351014	K562	blood:
5	22:31864703-31891033..22:32347255-32351014	K562	blood:
6	chr22:32346636..32349380-chr22:32349950..32352854,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238910	TF binding region
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000199248	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1049583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12168840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2246704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs2301415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2853884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2858752	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2858753	0.89[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs3747158	0.89[CHB][hapmap]
rs4820059	0.87[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4821004	0.83[MEX][hapmap]
rs5998196	0.89[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs7290696	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7291050	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7364274	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs738181	0.88[CHB][hapmap];1.00[LWK][hapmap]
rs8141011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];0.98[ASN][1000 genomes]
rs933226	0.88[CHB][hapmap]
rs9606887	0.80[ASN][1000 genomes]
rs9606888	0.80[ASN][1000 genomes]
rs9609394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609395	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9609397	1.00[YRI][hapmap]
rs9621371	0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]

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	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2858750	LIF	cis	cerebellum	SCAN
rs2858750	RFPL1	cis	cerebellum	SCAN
rs2858750	CHEK2	cis	cerebellum	SCAN
rs2858750	SEZ6L	cis	parietal	SCAN
rs2858750	YWHAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32342000-32354400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:32342400-32357600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32343400-32350400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr22:32343400-32355000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:32343600-32348800	Genic enhancers	K562	blood
6	chr22:32343600-32349200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:32343600-32349800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
8	chr22:32343600-32354600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:32343800-32351000	Strong transcription	Primary B cells from cord blood	blood
10	chr22:32344200-32349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr22:32344600-32352200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:32344800-32352000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:32345600-32349200	Genic enhancers	NHDF-Ad	bronchial
14	chr22:32345600-32350000	Enhancers	Fetal Brain Male	brain
15	chr22:32345600-32350800	Genic enhancers	HMEC	breast
16	chr22:32345600-32351200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr22:32345600-32351200	Genic enhancers	Fetal Brain Female	brain
18	chr22:32345800-32350000	Enhancers	Hela-S3	cervix
19	chr22:32345800-32351000	Genic enhancers	NHEK	skin
20	chr22:32345800-32351400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr22:32345800-32352600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr22:32346200-32349400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr22:32346200-32349400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr22:32346200-32350800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:32346200-32350800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr22:32346400-32349000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr22:32346400-32349000	Strong transcription	Brain Germinal Matrix	brain
28	chr22:32346400-32349000	Enhancers	Right Atrium	heart
29	chr22:32346400-32350600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr22:32346400-32351200	Genic enhancers	Rectal Mucosa Donor 31	rectum
31	chr22:32346600-32348400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
32	chr22:32346600-32348600	Genic enhancers	GM12878-XiMat	blood
33	chr22:32346600-32349000	Enhancers	Aorta	Aorta
34	chr22:32346600-32349000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr22:32346600-32351000	Enhancers	Colon Smooth Muscle	Colon
36	chr22:32346600-32351200	Enhancers	Brain Anterior Caudate	brain
37	chr22:32346600-32351600	Enhancers	HUVEC	blood vessel
38	chr22:32346600-32352200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:32346600-32352800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr22:32346600-32356400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr22:32346800-32348800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr22:32346800-32348800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr22:32346800-32348800	Enhancers	Right Ventricle	heart
44	chr22:32346800-32349000	Enhancers	HSMMtube	muscle
45	chr22:32346800-32350200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr22:32346800-32351200	Enhancers	Adipose Nuclei	Adipose
47	chr22:32346800-32351200	Enhancers	Stomach Mucosa	stomach
48	chr22:32346800-32351400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr22:32346800-32351400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr22:32346800-32352200	Enhancers	Primary T helper cells PMA-I stimulated	--

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