Variant report

Variant	rs9495596
Chromosome Location	chr6:140202822-140202823
allele	A/G
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	chr6:140202700-140203436	HCT-116	colon:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
2	RAD21	chr6:140202765-140203248	GM12878	blood:	n/a	chr6:140203206-140203220 chr6:140202987-140203006
3	CTCF	chr6:140202725-140203171	K562	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
4	RAD21	chr6:140202771-140203285	A549	lung:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
5	RAD21	chr6:140202644-140203346	MCF-7	breast:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
6	ARID3A	chr6:140202803-140203064	K562	blood:	n/a	n/a
7	CHD2	chr6:140202802-140203204	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr6:140202800-140202950	HFF-Myc	foreskin:	n/a	n/a
9	CTCF	chr6:140202769-140203154	SK-N-SH_RA	brain:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
10	RAD21	chr6:140202712-140203439	H1-hESC	embryonic stem cell:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
11	GATA3	chr6:140202692-140203771	SK-N-SH	brain:	n/a	chr6:140203511-140203520 chr6:140203410-140203421 chr6:140203709-140203719 chr6:140203510-140203520
12	SMC3	chr6:140202771-140203209	HepG2	liver:	n/a	n/a
13	RAD21	chr6:140202820-140203164	HepG2	liver:	n/a	chr6:140202987-140203006
14	SMC3	chr6:140202372-140204863	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr6:140202742-140203268	MCF-7	breast:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
16	CTCF	chr6:140202820-140202970	HCM	heart:	n/a	n/a
17	TCF12	chr6:140202717-140204825	SK-N-SH	brain:	n/a	n/a
18	ZNF143	chr6:140202820-140203152	GM12878	blood:	n/a	n/a
19	SIN3A	chr6:140202427-140203216	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr6:140202805-140203217	HepG2	liver:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
21	GATA3	chr6:140202786-140203171	T-47D	breast:	n/a	n/a
22	CTCF	chr6:140202641-140203224	GM12878	blood:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
23	RAD21	chr6:140202715-140203164	HepG2	liver:	n/a	chr6:140202987-140203006
24	CTCF	chr6:140202556-140203755	SK-N-SH	brain:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
25	RAD21	chr6:140202755-140203337	H1-hESC	embryonic stem cell:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
26	RAD21	chr6:140202792-140203155	GM12878	blood:	n/a	chr6:140202987-140203006
27	CTCF	chr6:140202799-140203350	HCT-116	colon:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
28	GATA3	chr6:140202790-140203924	SK-N-SH	brain:	n/a	chr6:140203511-140203520 chr6:140203410-140203421 chr6:140203709-140203719 chr6:140203510-140203520
29	RAD21	chr6:140202783-140203249	SK-N-SH_RA	brain:	n/a	chr6:140203206-140203220 chr6:140202987-140203006
30	CTCF	chr6:140202788-140203177	IMR90	lung:	n/a	chr6:140202988-140203009 chr6:140202986-140203004
31	TCF7L2	chr6:140202465-140203906	PANC-1	pancreas:	n/a	chr6:140202729-140202743 chr6:140203485-140203494 chr6:140203639-140203655
32	RAD21	chr6:140202781-140203306	ECC-1	luminal epithelium:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
33	RAD21	chr6:140202299-140204544	SK-N-SH	brain:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
34	RAD21	chr6:140202697-140203218	MCF-7	breast:	n/a	chr6:140202987-140203006
35	CTCF	chr6:140202820-140202970	NHEK	skin:	n/a	n/a
36	SMC3	chr6:140202787-140203573	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr6:140202753-140203880	SK-N-SH_RA	brain:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
38	RAD21	chr6:140202643-140203692	IMR90	lung:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
39	CTCF	chr6:140202740-140202890	A549	lung:	n/a	n/a
40	SMC3	chr6:140202799-140203360	GM12878	blood:	n/a	n/a
41	RAD21	chr6:140202730-140203270	A549	lung:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
42	RAD21	chr6:140202571-140203433	Hela-S3	cervix:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
43	RAD21	chr6:140202697-140203423	ECC-1	luminal epithelium:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006
44	RAD21	chr6:140202796-140203399	H1-hESC	embryonic stem cell:	n/a	chr6:140203206-140203220 chr6:140203246-140203260 chr6:140202987-140203006

No.	Distal block	Cell Line	Cell type
1	chr6:140202746..140205528-chr6:140208165..140210292,2	K562	blood:
2	chr6:139692335..139698075-chr6:140197375..140205470,17	MCF-7	breast:
3	chr6:140202740..140203385-chr6:140317580..140318152,2	MCF-7	breast:
4	chr6:140202203..140203486-chr6:140248180..140248949,4	MCF-7	breast:
5	chr6:140202515..140205528-chr6:140208165..140211710,3	K562	blood:
6	chr6:139692969..139697282-chr6:140197638..140202883,9	MCF-7	breast:
7	chr6:140202585..140203697-chr6:140762103..140763026,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225148	TF binding region
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10457036	0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10457699	1.00[JPT][hapmap]
rs10457701	0.90[ASN][1000 genomes]
rs10457702	0.81[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11155092	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155093	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155094	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754775	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193363	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193742	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194624	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194665	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198042	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198595	0.90[ASN][1000 genomes]
rs12198639	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198642	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202850	0.90[ASN][1000 genomes]
rs12204229	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204306	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12205335	0.90[ASN][1000 genomes]
rs12207470	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210493	0.90[ASN][1000 genomes]
rs12212554	0.90[ASN][1000 genomes]
rs12214000	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214369	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214414	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215417	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216315	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516775	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2024678	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064502	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34059065	0.90[ASN][1000 genomes]
rs72986764	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72986775	0.90[ASN][1000 genomes]
rs9373254	0.91[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs9376479	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484322	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9495596	IL22RA2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140190800-140203400	Weak transcription	Fetal Lung	lung
2	chr6:140191600-140203000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:140194400-140203000	Weak transcription	NHLF	lung
4	chr6:140194800-140204200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:140201000-140206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:140201200-140203000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:140201200-140203200	Weak transcription	Placenta	Placenta
8	chr6:140201400-140203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:140201400-140203000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:140201400-140203400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:140201400-140204200	Weak transcription	Liver	Liver
12	chr6:140201600-140203000	Weak transcription	K562	blood
13	chr6:140201800-140203200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:140201800-140203200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:140201800-140205000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr6:140201800-140206400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:140202000-140203200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:140202000-140203800	Enhancers	Brain Germinal Matrix	brain
19	chr6:140202000-140209000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:140202000-140209600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:140202200-140204400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:140202200-140205000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr6:140202200-140206400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:140202400-140203000	Enhancers	Brain Hippocampus Middle	brain
25	chr6:140202400-140203200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:140202400-140203200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:140202400-140203200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:140202400-140203400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:140202400-140203600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:140202400-140203800	Weak transcription	Fetal Kidney	kidney
31	chr6:140202400-140204000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:140202400-140205000	Enhancers	Brain Anterior Caudate	brain
33	chr6:140202400-140205200	Enhancers	Brain Substantia Nigra	brain
34	chr6:140202400-140205400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr6:140202400-140205600	Enhancers	Fetal Heart	heart
36	chr6:140202400-140205600	Enhancers	HSMM	muscle
37	chr6:140202400-140206000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:140202400-140206400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:140202400-140211800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:140202600-140203000	Enhancers	Osteobl	bone
41	chr6:140202600-140203200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:140202600-140205200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:140202600-140205800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:140202600-140206400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr6:140202800-140203000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr6:140202800-140203400	Weak transcription	Brain Inferior Temporal Lobe	brain

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