Variant report

Variant	rs9470228
Chromosome Location	chr6:36163941-36163942
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	RUNX3	chr6:36163750-36164537	GM12878	blood:	n/a	n/a
2	MAX	chr6:36163879-36164692	A549	lung:	n/a	chr6:36164451-36164461 chr6:36164162-36164171
3	POLR2A	chr6:36163833-36165846	K562	blood:	n/a	n/a
4	CTCF	chr6:36163840-36163990	AG09309	skin:	n/a	n/a
5	RCOR1	chr6:36163929-36164316	K562	blood:	n/a	n/a
6	MAFK	chr6:36163742-36164050	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:36163762-36165393	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr6:36163770-36165445	PANC-1	pancreas:	n/a	n/a
9	ZBTB7A	chr6:36163893-36165546	ECC-1	luminal epithelium:	n/a	chr6:36165054-36165061
10	RUNX3	chr6:36163557-36164451	GM12878	blood:	n/a	n/a
11	MAX	chr6:36163895-36164792	ECC-1	luminal epithelium:	n/a	chr6:36164451-36164461 chr6:36164162-36164171
12	MAZ	chr6:36163880-36165266	Hela-S3	cervix:	n/a	chr6:36165011-36165021 chr6:36164451-36164461 chr6:36164162-36164171
13	FOXA1	chr6:36163532-36164454	HepG2	liver:	n/a	n/a
14	REST	chr6:36163332-36165694	H1-neurons	neurons:	n/a	n/a
15	JUND	chr6:36163680-36164383	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr6:36163853-36165707	K562	blood:	n/a	chr6:36165011-36165021 chr6:36164451-36164461 chr6:36164162-36164171
17	CREB1	chr6:36163586-36165456	HepG2	liver:	n/a	chr6:36164052-36164065
18	CBX3	chr6:36163726-36164276	K562	blood:	n/a	n/a
19	POLR2A	chr6:36163339-36165840	HepG2	liver:	n/a	n/a
20	STAT1	chr6:36163875-36164396	GM12878	blood:	n/a	n/a
21	RAD21	chr6:36163905-36164573	MCF-7	breast:	n/a	chr6:36164174-36164187 chr6:36164248-36164262
22	POLR2A	chr6:36163879-36163954	A549	lung:	n/a	n/a
23	TAF1	chr6:36163926-36165357	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr6:36163784-36165406	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr6:36163796-36165332	MCF-7	breast:	n/a	n/a
26	CTCF	chr6:36163936-36164470	K562	blood:	n/a	chr6:36164246-36164264
27	POLR2A	chr6:36163781-36165389	MCF-7	breast:	n/a	n/a
28	CTCF	chr6:36163814-36164428	H1-hESC	embryonic stem cell:	n/a	chr6:36164246-36164264
29	TBP	chr6:36163857-36165390	H1-hESC	embryonic stem cell:	n/a	n/a
30	BCLAF1	chr6:36163899-36164515	GM12878	blood:	n/a	chr6:36164234-36164243 chr6:36164197-36164210
31	NRF1	chr6:36163407-36164564	SK-N-SH	brain:	n/a	chr6:36164237-36164246 chr6:36164170-36164179
32	POLR2A	chr6:36163834-36165437	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr6:36163920-36164070	RPTEC	kidney:	n/a	n/a
34	POLR2A	chr6:36163833-36165525	H1-hESC	embryonic stem cell:	n/a	n/a
35	HEY1	chr6:36163875-36165373	K562	blood:	n/a	chr6:36165006-36165021 chr6:36164530-36164545 chr6:36164234-36164249
36	RAD21	chr6:36163922-36164425	HepG2	liver:	n/a	chr6:36164174-36164187 chr6:36164248-36164262
37	MAX	chr6:36163798-36164398	NB4	blood:	n/a	chr6:36164162-36164171
38	ZBTB7A	chr6:36163863-36165308	K562	blood:	n/a	chr6:36165054-36165061
39	POLR2A	chr6:36163766-36164312	H1-hESC	embryonic stem cell:	n/a	n/a
40	CHD2	chr6:36163750-36164382	GM12878	blood:	n/a	n/a
41	MAX	chr6:36163633-36164688	MCF-7	breast:	n/a	chr6:36164451-36164461 chr6:36164162-36164171
42	ZNF263	chr6:36163924-36164666	HEK293-T-REx	kidney:	n/a	n/a
43	SIN3A	chr6:36163624-36165355	H1-hESC	embryonic stem cell:	n/a	n/a
44	HNF4G	chr6:36163690-36164381	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:36163759-36164014	HCT-116	colon:	n/a	n/a
46	HEY1	chr6:36163573-36164786	HepG2	liver:	n/a	chr6:36164530-36164545 chr6:36164234-36164249
47	ZNF384	chr6:36163551-36164070	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:36163776-36165421	GM12878	blood:	n/a	n/a
49	NR2F2	chr6:36163621-36164295	K562	blood:	n/a	n/a
50	HDAC2	chr6:36163826-36164481	MCF-7	breast:	n/a	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	chr6:36152501..36154693-chr6:36162205..36164087,2	MCF-7	breast:
5	chr6:36097672..36103046-chr6:36163327..36166048,5	MCF-7	breast:
6	chr6:36089979..36090632-chr6:36163721..36164348,2	MCF-7	breast:
7	chr6:36098131..36102554-chr6:36163258..36166179,4	K562	blood:
8	chr6:35993265..35998448-chr6:36161633..36166981,11	K562	blood:
9	chr16:68271616..68273577-chr6:36163527..36165172,2	MCF-7	breast:
10	chr6:35994949..35995828-chr6:36163769..36164278,2	K562	blood:
11	chr6:36083240..36096353-chr6:36161490..36168411,30	MCF-7	breast:
12	chr6:36097129..36099054-chr6:36162391..36164603,2	K562	blood:
13	chr6:36105269..36110195-chr6:36162724..36166768,9	MCF-7	breast:
14	chr6:36093292..36096677-chr6:36162699..36165787,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf222-1	chr6:36163814-36163947	ENSG00000246982
2	lnc-C6orf222-1	chr6:36163814-36164288	NONHSAT112212
3	lnc-C6orf222-1	chr6:36163814-36163947	ENSG00000246982

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

Extended variants
information (count: 21 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10807157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947591	0.84[EUR][1000 genomes]
rs2032506	0.93[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2301422	0.83[EUR][1000 genomes]
rs4236048	0.93[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs61435713	0.86[AFR][1000 genomes]
rs6457884	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6457892	0.87[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6457894	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs6906612	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73413695	0.81[AFR][1000 genomes]
rs7747793	0.93[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7754042	0.86[ASW][hapmap];0.97[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs7773924	0.84[EUR][1000 genomes]
rs7775197	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs9296177	0.93[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs9366900	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470224	0.87[ASW][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9470228	BAK1	cis	cerebellum	SCAN
rs9470228	PNPLA1	cis	parietal	SCAN
rs9470228	RP1-179N16.6	cis	Nerve Tibial	GTEx
rs9470228	RP1-179N16.6	cis	Adipose Subcutaneous	GTEx
rs9470228	TMEM217	cis	cerebellum	SCAN
rs9470228	MAPK13	cis	parietal	SCAN
rs9470228	RP1-179N16.6	cis	Artery Tibial	GTEx
rs9470228	RP1-179N16.6	cis	Stomach	GTEx

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	chr6:36163400-36164000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:36163400-36164000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:36163400-36164000	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr6:36163400-36164200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr6:36163400-36164200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr6:36163400-36164200	Active TSS	Fetal Brain Male	brain
10	chr6:36163400-36164200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:36163400-36164200	Flanking Active TSS	Dnd41	blood
12	chr6:36163400-36164400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:36163400-36164400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr6:36163400-36165600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:36163400-36165600	Active TSS	Fetal Brain Female	brain
16	chr6:36163400-36165600	Active TSS	Fetal Intestine Large	intestine
17	chr6:36163400-36166000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr6:36163400-36166200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:36163400-36166400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:36163400-36166400	Active TSS	Fetal Kidney	kidney
21	chr6:36163600-36164000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:36163600-36164000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:36163600-36164000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:36163600-36164000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:36163600-36164000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:36163600-36164000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:36163600-36164000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:36163600-36164000	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr6:36163600-36164000	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr6:36163600-36164000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr6:36163600-36164000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:36163600-36164000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr6:36163600-36164000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:36163600-36164000	Active TSS	Stomach Mucosa	stomach
35	chr6:36163600-36164200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr6:36163600-36164200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr6:36163600-36164200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:36163600-36164200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr6:36163600-36164200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr6:36163600-36164200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:36163600-36164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:36163600-36164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:36163600-36164200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr6:36163600-36164200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:36163600-36164200	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr6:36163600-36164200	Flanking Active TSS	Fetal Thymus	thymus
47	chr6:36163600-36164200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr6:36163600-36164200	Flanking Active TSS	GM12878-XiMat	blood
49	chr6:36163600-36164200	Flanking Active TSS	HUVEC	blood vessel
50	chr6:36163600-36164200	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links