Variant report

Variant	rs5998300
Chromosome Location	chr22:32602718-32602719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr22:32602297-32603340	SK-N-SH	brain:	n/a	chr22:32603056-32603070 chr22:32603061-32603070 chr22:32603052-32603071
2	SIN3A	chr22:32602406-32602725	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr22:32601991-32603467	SK-N-SH	brain:	n/a	chr22:32603055-32603071 chr22:32603049-32603070 chr22:32603061-32603068 chr22:32603054-32603072 chr22:32602699-32602707 chr22:32603056-32603069
4	CTCF	chr22:32602202-32602818	A549	lung:	n/a	chr22:32602699-32602707
5	CTCF	chr22:32602311-32602764	HepG2	liver:	n/a	chr22:32602699-32602707
6	CTCF	chr22:32602600-32602750	HAc	cerebellar:	n/a	chr22:32602699-32602707
7	CTCF	chr22:32602351-32603315	K562	blood:	n/a	chr22:32603055-32603071 chr22:32603049-32603070 chr22:32603061-32603068 chr22:32603054-32603072 chr22:32602699-32602707 chr22:32603056-32603069
8	CTCF	chr22:32602700-32602850	GM12875	blood:	n/a	n/a
9	CTCF	chr22:32602701-32602770	GM19238	blood:	n/a	n/a
10	CTCF	chr22:32602580-32602730	NB4	blood:	n/a	chr22:32602699-32602707
11	CTCF	chr22:32602391-32602722	HepG2	liver:	n/a	chr22:32602699-32602707
12	CTCF	chr22:32602620-32602770	HUVEC	blood vessel:	n/a	chr22:32602699-32602707
13	CTCF	chr22:32602308-32602780	H1-hESC	embryonic stem cell:	n/a	chr22:32602699-32602707
14	ZNF143	chr22:32602454-32603274	H1-hESC	embryonic stem cell:	n/a	chr22:32603005-32603023
15	RAD21	chr22:32602324-32602758	H1-hESC	embryonic stem cell:	n/a	n/a
16	SMC3	chr22:32602302-32603454	SK-N-SH	brain:	n/a	chr22:32603056-32603070
17	CTCF	chr22:32602580-32602730	AG10803	skin:	n/a	chr22:32602699-32602707
18	CTCF	chr22:32602317-32602767	H1-hESC	embryonic stem cell:	n/a	chr22:32602699-32602707
19	CTCF	chr22:32602316-32603398	HCT-116	colon:	n/a	chr22:32603055-32603071 chr22:32603049-32603070 chr22:32603061-32603068 chr22:32603054-32603072 chr22:32602699-32602707 chr22:32603056-32603069

No.	Distal block	Cell Line	Cell type
1	chr22:32586637..32588277-chr22:32602438..32604395,2	K562	blood:
2	chr22:32537081..32537949-chr22:32602635..32603271,2	MCF-7	breast:
3	22:31936958-31958600..22:32594665-32606395	K562	blood:
4	chr22:32601130..32602920-chr22:32660025..32662874,2	MCF-7	breast:

Variant related genes	Relation type
RFPL2	TF binding region
ENSG00000214093	Chromatin interaction
ENSG00000239674	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12157791	1.00[JPT][hapmap]
rs12160108	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12160790	1.00[JPT][hapmap]
rs16989807	1.00[CHB][hapmap]
rs16989809	1.00[CHB][hapmap]
rs16989893	1.00[CHB][hapmap]
rs16990001	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16990004	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16990065	1.00[JPT][hapmap]
rs16990066	1.00[JPT][hapmap]
rs2179066	1.00[JPT][hapmap]
rs2235168	1.00[JPT][hapmap]
rs2235171	0.89[JPT][hapmap]
rs2294205	1.00[JPT][hapmap]
rs2294206	1.00[JPT][hapmap]
rs2294207	1.00[JPT][hapmap]
rs2294211	0.89[JPT][hapmap]
rs57468334	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5994491	1.00[JPT][hapmap]
rs5994496	1.00[JPT][hapmap]
rs5994502	1.00[JPT][hapmap]
rs5994503	1.00[JPT][hapmap]
rs5994511	1.00[JPT][hapmap]
rs5994512	1.00[JPT][hapmap]
rs5998317	0.89[JPT][hapmap]
rs5998318	0.86[JPT][hapmap]
rs5998321	1.00[JPT][hapmap]
rs5998326	1.00[JPT][hapmap]
rs5998329	1.00[JPT][hapmap]
rs7287853	1.00[JPT][hapmap]
rs7292474	0.91[CEU][hapmap]
rs760556	0.86[ASN][1000 genomes]
rs8137034	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv834178	chr22:32490449-32677521	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv3597	chr22:32588424-32632724	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv2753006	chr22:32592120-32719481	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32598400-32602800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr22:32598600-32603400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:32600000-32603200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr22:32600800-32602800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr22:32600800-32602800	Weak transcription	Pancreas	Pancrea
6	chr22:32600800-32603000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:32600800-32603200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr22:32600800-32603600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr22:32600800-32622800	Weak transcription	Right Atrium	heart
10	chr22:32601000-32603000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr22:32601000-32603000	Active TSS	HepG2	liver
12	chr22:32601200-32602800	Weak transcription	Esophagus	oesophagus
13	chr22:32601200-32603000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr22:32601200-32603000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr22:32601200-32603200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr22:32601200-32603400	Enhancers	Liver	Liver
17	chr22:32601200-32605200	Weak transcription	Gastric	stomach
18	chr22:32601600-32602800	Enhancers	Fetal Brain Male	brain
19	chr22:32601600-32603000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr22:32601600-32603200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr22:32601600-32603400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr22:32601600-32603400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr22:32601800-32602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:32601800-32603400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr22:32601800-32604800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr22:32601800-32608600	Weak transcription	Brain Angular Gyrus	brain
27	chr22:32602200-32603000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr22:32602200-32603200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:32602200-32603200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr22:32602200-32603200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr22:32602200-32603400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr22:32602200-32603800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr22:32602200-32621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:32602400-32602800	Flanking Active TSS	A549	lung
35	chr22:32602400-32603000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr22:32602400-32603000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr22:32602400-32603600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr22:32602400-32605600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr22:32602400-32606200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:32602600-32602800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
41	chr22:32602600-32602800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr22:32602600-32603000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr22:32602600-32603000	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr22:32602600-32603200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr22:32602600-32603400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:32602600-32603600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr22:32602600-32603600	Enhancers	Spleen	Spleen

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