Variant report

Variant	rs9470229
Chromosome Location	chr6:36164092-36164093
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	POLR2A	chr6:36163994-36165667	IMR90	lung:	n/a	n/a
2	RAD21	chr6:36164046-36164397	GM12878	blood:	n/a	chr6:36164174-36164187 chr6:36164248-36164262
3	RUNX3	chr6:36163750-36164537	GM12878	blood:	n/a	n/a
4	MAX	chr6:36163879-36164692	A549	lung:	n/a	chr6:36164451-36164461 chr6:36164162-36164171
5	RAD21	chr6:36163953-36164467	IMR90	lung:	n/a	chr6:36164174-36164187 chr6:36164248-36164262
6	POLR2A	chr6:36163833-36165846	K562	blood:	n/a	n/a
7	POLR2A	chr6:36163984-36165348	HUVEC	blood vessel:	n/a	n/a
8	RCOR1	chr6:36163929-36164316	K562	blood:	n/a	n/a
9	MYC	chr6:36164044-36164576	MCF-7	breast:	n/a	chr6:36164451-36164461 chr6:36164162-36164171
10	POLR2A	chr6:36163762-36165393	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr6:36163770-36165445	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr6:36163977-36165400	Hela-S3	cervix:	n/a	n/a
13	YY1	chr6:36163961-36165258	K562	blood:	n/a	chr6:36165010-36165019 chr6:36165007-36165016 chr6:36164526-36164540 chr6:36164701-36164715
14	ZBTB7A	chr6:36163893-36165546	ECC-1	luminal epithelium:	n/a	chr6:36165054-36165061
15	GATA3	chr6:36163988-36164355	T-47D	breast:	n/a	chr6:36164077-36164087
16	RUNX3	chr6:36163557-36164451	GM12878	blood:	n/a	n/a
17	RAD21	chr6:36164021-36164450	A549	lung:	n/a	chr6:36164174-36164187 chr6:36164248-36164262
18	MAX	chr6:36163895-36164792	ECC-1	luminal epithelium:	n/a	chr6:36164451-36164461 chr6:36164162-36164171
19	MAZ	chr6:36163880-36165266	Hela-S3	cervix:	n/a	chr6:36165011-36165021 chr6:36164451-36164461 chr6:36164162-36164171
20	PAX5	chr6:36164045-36164293	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:36163968-36165403	HUVEC	blood vessel:	n/a	n/a
22	SIN3AK20	chr6:36164010-36164275	SK-N-SH	brain:	n/a	n/a
23	FOXA1	chr6:36163532-36164454	HepG2	liver:	n/a	n/a
24	REST	chr6:36163332-36165694	H1-neurons	neurons:	n/a	n/a
25	JUND	chr6:36163680-36164383	H1-hESC	embryonic stem cell:	n/a	n/a
26	POU2F2	chr6:36163962-36164427	GM12891	blood:	n/a	n/a
27	SMC3	chr6:36164028-36164408	GM12878	blood:	n/a	n/a
28	MAX	chr6:36163853-36165707	K562	blood:	n/a	chr6:36165011-36165021 chr6:36164451-36164461 chr6:36164162-36164171
29	POLR2A	chr6:36164074-36165420	PFSK-1	brain:	n/a	n/a
30	CREB1	chr6:36163586-36165456	HepG2	liver:	n/a	chr6:36164052-36164065
31	CBX3	chr6:36163726-36164276	K562	blood:	n/a	n/a
32	MAFK	chr6:36163974-36164203	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr6:36163339-36165840	HepG2	liver:	n/a	n/a
34	STAT1	chr6:36163875-36164396	GM12878	blood:	n/a	n/a
35	E2F6	chr6:36163958-36164668	K562	blood:	n/a	chr6:36164381-36164388 chr6:36164381-36164388 chr6:36164380-36164388 chr6:36164237-36164246 chr6:36164381-36164388
36	POLR2A	chr6:36163987-36165374	K562	blood:	n/a	n/a
37	RAD21	chr6:36163905-36164573	MCF-7	breast:	n/a	chr6:36164174-36164187 chr6:36164248-36164262
38	TAF1	chr6:36163926-36165357	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr6:36163784-36165406	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr6:36163796-36165332	MCF-7	breast:	n/a	n/a
41	YY1	chr6:36164061-36164454	GM12891	blood:	n/a	n/a
42	CTCF	chr6:36163936-36164470	K562	blood:	n/a	chr6:36164246-36164264
43	POLR2A	chr6:36163967-36165358	Hela-S3	cervix:	n/a	n/a
44	ELF1	chr6:36163972-36165332	GM12878	blood:	n/a	chr6:36165006-36165018 chr6:36164523-36164532
45	POLR2A	chr6:36163781-36165389	MCF-7	breast:	n/a	n/a
46	CTCF	chr6:36164000-36164150	GM12872	blood:	n/a	n/a
47	CTCF	chr6:36163814-36164428	H1-hESC	embryonic stem cell:	n/a	chr6:36164246-36164264
48	TAF1	chr6:36164065-36165262	K562	blood:	n/a	n/a
49	CTCF	chr6:36164083-36164386	A549	lung:	n/a	chr6:36164246-36164264
50	HCFC1	chr6:36164066-36164457	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:36164058-36164108	A549	lung:	n/a
2	chr6:36164058-36164108	HepG2	liver:	n/a
3	chr6:36164058-36164108	U87	brain:	n/a
4	chr6:36164058-36164108	SAEC	small airway:	n/a
5	chr6:36164058-36164108	HCPEpiC	choroid plexus:	n/a
6	chr6:36164058-36164108	NH-A	brain:	n/a
7	chr6:36164058-36164108	Hepatocyte	liver:	n/a
8	chr6:36164058-36164108	IMR90	lung:	fetal
9	chr6:36164058-36164108	NB4	blood:	n/a
10	chr6:36164058-36164108	Hela-S3	cervix:	n/a
11	chr6:36164058-36164108	NHDF-neo	bronchial:	n/a
12	chr6:36164058-36164108	T-47D	breast:	n/a
13	chr6:36164058-36164108	BE2_C	brain:	n/a
14	chr6:36164058-36164108	SK-N-SH_RA	brain:	n/a
15	chr6:36164058-36164108	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:36164058-36164108	CMK	blood:	n/a
17	chr6:36164058-36164108	AG04449	skin:	fetal
18	chr6:36164058-36164108	HL-60	blood:	n/a
19	chr6:36164058-36164108	ovcar-3	ovarian:	n/a
20	chr6:36164058-36164108	Jurkat	blood:	n/a
21	chr6:36164058-36164108	HCT-116	colon:	n/a
22	chr6:36164058-36164108	AG09309	skin:	n/a
23	chr6:36164058-36164108	HRE	kidney:	n/a
24	chr6:36164058-36164108	HEK293	kidney:	embryo
25	chr6:36164058-36164108	AG09319	gingival:	n/a
26	chr6:36164058-36164108	NHBE	bronchial:	n/a
27	chr6:36164058-36164108	SK-N-SH	brain:	n/a
28	chr6:36164058-36164108	GM19239	blood:	n/a
29	chr6:36164058-36164108	AG10803	skin:	n/a
30	chr6:36164058-36164108	GM12878	blood:	n/a
31	chr6:36164058-36164108	HRPEpiC	eye:	n/a
32	chr6:36164058-36164108	HNPCEpiC	eye:	n/a
33	chr6:36164058-36164108	MCF10A-Er-Src	breast:	n/a
34	chr6:36164058-36164108	HMEC	breast:	n/a
35	chr6:36164058-36164108	AoSMC	blood vessel:	n/a
36	chr6:36164058-36164108	GM12891	blood:	n/a
37	chr6:36164058-36164108	HEEpiC	esophagus:	n/a
38	chr6:36164058-36164108	HCF	heart:	n/a
39	chr6:36164058-36164108	LNCaP	prostate:	n/a
40	chr6:36164058-36164108	RPTEC	kidney:	n/a
41	chr6:36164058-36164108	BJ	skin:	n/a
42	chr6:36164058-36164108	MCF-7	breast:	n/a
43	chr6:36164058-36164108	SK-N-MC	brain:	n/a
44	chr6:36164058-36164108	PANC-1	pancreas:	n/a
45	chr6:36164058-36164108	HRCEpiC	kidney:	n/a
46	chr6:36164058-36164108	PFSK-1	brain:	n/a
47	chr6:36164058-36164108	GM06990	blood:	n/a
48	chr6:36164058-36164108	PrEC	prostate:	n/a
49	chr6:36164058-36164108	ECC-1	luminal epithelium:	n/a
50	chr6:36164058-36164108	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:35992707..35998254-chr6:36162958..36166458,7	K562	blood:
2	chr6:35993989..35997402-chr6:36163188..36166883,8	MCF-7	breast:
3	chr6:36096617..36099142-chr6:36162886..36164936,2	MCF-7	breast:
4	chr6:36097672..36103046-chr6:36163327..36166048,5	MCF-7	breast:
5	chr6:36089979..36090632-chr6:36163721..36164348,2	MCF-7	breast:
6	chr6:36098131..36102554-chr6:36163258..36166179,4	K562	blood:
7	chr6:35993265..35998448-chr6:36161633..36166981,11	K562	blood:
8	chr16:68271616..68273577-chr6:36163527..36165172,2	MCF-7	breast:
9	chr6:35994949..35995828-chr6:36163769..36164278,2	K562	blood:
10	chr6:36083240..36096353-chr6:36161490..36168411,30	MCF-7	breast:
11	chr6:36097129..36099054-chr6:36162391..36164603,2	K562	blood:
12	chr6:36105269..36110195-chr6:36162724..36166768,9	MCF-7	breast:
13	chr6:36093292..36096677-chr6:36162699..36165787,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf222-1	chr6:36163814-36164288	NONHSAT112212

Variant related genes	Relation type
BRPF3	TF binding region
BRPF3	CpG island
ENSG00000221743	Chromatin interaction
ENSG00000156711	Chromatin interaction
ENSG00000103067	Chromatin interaction
ENSG00000112062	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2239798	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2815807	0.83[MKK][hapmap]
rs2859129	0.80[CEU][hapmap];0.86[MKK][hapmap]
rs2859131	0.80[CEU][hapmap];0.86[MKK][hapmap]
rs4236049	0.88[ASW][hapmap];0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4395718	0.83[ASW][hapmap];0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs4713940	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4713941	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs59200830	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9462161	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs9462162	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9462164	0.94[ASW][hapmap];0.89[CHD][hapmap];1.00[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs9462165	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470222	0.87[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[MKK][hapmap]
rs9470226	0.86[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs9470230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470233	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470234	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470235	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3355640	chr6:36163199-36165747	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3418753	chr6:36163624-36166272	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9470229	ANKS1A	cis	cerebellum	SCAN
rs9470229	MAPK14	cis	cerebellum	SCAN
rs9470229	C6orf222	cis	parietal	SCAN
rs9470229	MAPK13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36163000-36165800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:36163200-36165800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:36163200-36166200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:36163400-36164200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr6:36163400-36164200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr6:36163400-36164200	Active TSS	Fetal Brain Male	brain
7	chr6:36163400-36164200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr6:36163400-36164200	Flanking Active TSS	Dnd41	blood
9	chr6:36163400-36164400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:36163400-36164400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:36163400-36165600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:36163400-36165600	Active TSS	Fetal Brain Female	brain
13	chr6:36163400-36165600	Active TSS	Fetal Intestine Large	intestine
14	chr6:36163400-36166000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:36163400-36166200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:36163400-36166400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:36163400-36166400	Active TSS	Fetal Kidney	kidney
18	chr6:36163600-36164200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr6:36163600-36164200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr6:36163600-36164200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr6:36163600-36164200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr6:36163600-36164200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr6:36163600-36164200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:36163600-36164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:36163600-36164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:36163600-36164200	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr6:36163600-36164200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:36163600-36164200	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr6:36163600-36164200	Flanking Active TSS	Fetal Thymus	thymus
30	chr6:36163600-36164200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr6:36163600-36164200	Flanking Active TSS	GM12878-XiMat	blood
32	chr6:36163600-36164200	Flanking Active TSS	HUVEC	blood vessel
33	chr6:36163600-36164200	Flanking Active TSS	K562	blood
34	chr6:36163600-36164200	Flanking Active TSS	NHEK	skin
35	chr6:36163600-36164200	Flanking Active TSS	Osteobl	bone
36	chr6:36163600-36165400	Active TSS	Placenta Amnion	Placenta Amnion
37	chr6:36163600-36165600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:36163600-36165600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:36163600-36165600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:36163600-36165600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr6:36163600-36165600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:36163600-36165600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:36163600-36165600	Active TSS	Brain Angular Gyrus	brain
44	chr6:36163600-36165600	Active TSS	Brain Substantia Nigra	brain
45	chr6:36163600-36165600	Active TSS	Colon Smooth Muscle	Colon
46	chr6:36163600-36165600	Active TSS	Fetal Stomach	stomach
47	chr6:36163600-36165600	Active TSS	Psoas Muscle	Psoas
48	chr6:36163600-36165600	Active TSS	Stomach Smooth Muscle	stomach
49	chr6:36163600-36165800	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:36163600-36165800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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