Variant report

Variant	rs3094220
Chromosome Location	chr6:31082987-31082988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:179)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:179 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:31082956-31083073	MCF-7	breast:	n/a	n/a
2	SMARCC1	chr6:31081841-31083341	Hela-S3	cervix:	n/a	chr6:31082449-31082458
3	CTCF	chr6:31082936-31083029	GM13976	blood:	n/a	n/a
4	CTCF	chr6:31082940-31083090	BJ	skin:	n/a	n/a
5	CTCF	chr6:31082880-31083030	Caco-2	colon:	n/a	n/a
6	RAD21	chr6:31082699-31083229	A549	lung:	n/a	n/a
7	FOS	chr6:31082302-31083000	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
8	FOSL1	chr6:31082011-31083367	HCT-116	colon:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
9	CTCF	chr6:31082920-31083070	GM12864	blood:	n/a	n/a
10	CTCF	chr6:31082900-31083050	HepG2	liver:	n/a	n/a
11	CTCF	chr6:31082900-31083050	BE2_C	brain:	n/a	n/a
12	YY1	chr6:31082694-31083093	SK-N-SH_RA	brain:	n/a	chr6:31082828-31082838
13	CTCF	chr6:31082900-31083050	HMEC	breast:	n/a	n/a
14	CTCF	chr6:31082880-31083030	HMF	breast:	n/a	n/a
15	ZNF143	chr6:31082351-31083154	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr6:31082359-31083165	Hela-S3	cervix:	n/a	chr6:31082419-31082433
17	SMC3	chr6:31082344-31083304	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr6:31082920-31083070	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr6:31082860-31083010	HA-sp	spinal cord:	n/a	n/a
20	MXI1	chr6:31082449-31083233	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr6:31082877-31083100	A549	lung:	n/a	n/a
22	CTCF	chr6:31082942-31083091	GM12891	blood:	n/a	n/a
23	CTCF	chr6:31082900-31083050	SK-N-SH_RA	brain:	n/a	n/a
24	RAD21	chr6:31082738-31083228	MCF-7	breast:	n/a	n/a
25	CTCF	chr6:31082920-31083070	SAEC	small airway:	n/a	n/a
26	CTCF	chr6:31082880-31083030	SAEC	small airway:	n/a	n/a
27	CTCF	chr6:31082900-31083050	AG04450	lung:	n/a	n/a
28	CTCF	chr6:31082940-31083090	AoAF	blood vessel:	n/a	n/a
29	CTCF	chr6:31082960-31083110	HMF	breast:	n/a	n/a
30	CTCF	chr6:31082881-31083103	Gliobla	brain:	n/a	n/a
31	CTCF	chr6:31082940-31083090	A549	lung:	n/a	n/a
32	CTCF	chr6:31082652-31083345	A549	lung:	n/a	n/a
33	YY1	chr6:31082669-31083116	SK-N-SH_RA	brain:	n/a	chr6:31082828-31082838
34	CTCF	chr6:31082857-31083036	K562	blood:	n/a	n/a
35	RAD21	chr6:31082847-31083110	HepG2	liver:	n/a	n/a
36	CTCF	chr6:31082920-31083070	MCF-7	breast:	n/a	n/a
37	CTCF	chr6:31082880-31083030	HCFaa	heart:	n/a	n/a
38	CTCF	chr6:31082920-31083070	HPAF	blood vessel:	n/a	n/a
39	CTCF	chr6:31082893-31083029	Lung_OC	lung:	n/a	n/a
40	CTCF	chr6:31082707-31083128	MCF-7	breast:	n/a	n/a
41	CTCF	chr6:31082918-31083045	GM19240	blood:	n/a	n/a
42	CTCF	chr6:31082805-31083137	K562	blood:	n/a	n/a
43	CTCF	chr6:31082864-31083141	NHEK	skin:	n/a	n/a
44	CTCF	chr6:31082940-31083090	HAc	cerebellar:	n/a	n/a
45	CTCF	chr6:31082914-31083022	GM13977	blood:	n/a	n/a
46	CTCF	chr6:31082924-31083020	Kidney_OC	kidney:	n/a	n/a
47	CTCF	chr6:31082722-31083245	K562	blood:	n/a	n/a
48	CTCF	chr6:31082851-31083105	Hela-S3	cervix:	n/a	n/a
49	RAD21	chr6:31082669-31083113	MCF-7	breast:	n/a	n/a
50	CTCF	chr6:31082870-31083089	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31082939-31082989	K562	blood:	n/a
2	chr6:31082939-31082989	HNPCEpiC	eye:	n/a
3	chr6:31082939-31082989	Jurkat	blood:	n/a
4	chr6:31082939-31082989	HCPEpiC	choroid plexus:	n/a
5	chr6:31082939-31082989	IMR90	lung:	fetal
6	chr6:31082939-31082989	AG04450	lung:	fetal
7	chr6:31082939-31082989	GM12892	blood:	n/a
8	chr6:31082939-31082989	GM12878	blood:	n/a
9	chr6:31082939-31082989	GM06990	blood:	n/a
10	chr6:31082939-31082989	MCF10A-Er-Src	breast:	n/a
11	chr6:31082939-31082989	LNCaP	prostate:	n/a
12	chr6:31082939-31082989	PANC-1	pancreas:	n/a
13	chr6:31082939-31082989	SK-N-MC	brain:	n/a
14	chr6:31082939-31082989	HMEC	breast:	n/a
15	chr6:31082939-31082989	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:31082939-31082989	Caco-2	colon:	n/a
17	chr6:31082939-31082989	NHDF-neo	bronchial:	n/a
18	chr6:31082939-31082989	NB4	blood:	n/a
19	chr6:31082939-31082989	GM19239	blood:	n/a
20	chr6:31082939-31082989	Hela-S3	cervix:	n/a
21	chr6:31082939-31082989	SK-N-SH	brain:	n/a
22	chr6:31082939-31082989	HIPEpiC	eye:	n/a
23	chr6:31082939-31082989	RPTEC	kidney:	n/a
24	chr6:31082939-31082989	HEEpiC	esophagus:	n/a
25	chr6:31082939-31082989	PrEC	prostate:	n/a
26	chr6:31082939-31082989	NHBE	bronchial:	n/a
27	chr6:31082939-31082989	HCM	heart:	n/a
28	chr6:31082939-31082989	AG09309	skin:	n/a
29	chr6:31082939-31082989	AG09319	gingival:	n/a
30	chr6:31082939-31082989	T-47D	breast:	n/a
31	chr6:31082939-31082989	ECC-1	luminal epithelium:	n/a
32	chr6:31082939-31082989	AG10803	skin:	n/a
33	chr6:31082939-31082989	MCF-7	breast:	n/a
34	chr6:31082939-31082989	HCF	heart:	n/a
35	chr6:31082939-31082989	SKMC	muscle:	n/a
36	chr6:31082939-31082989	HepG2	liver:	n/a
37	chr6:31082939-31082989	SAEC	small airway:	n/a
38	chr6:31082939-31082989	CMK	blood:	n/a
39	chr6:31082939-31082989	HEK293	kidney:	embryo
40	chr6:31082939-31082989	NT2-D1	testis:	n/a
41	chr6:31082939-31082989	SK-N-SH_RA	brain:	n/a
42	chr6:31082939-31082989	HUVEC	blood vessel:	n/a
43	chr6:31082939-31082989	BE2_C	brain:	n/a
44	chr6:31082939-31082989	AG04449	skin:	fetal
45	chr6:31082939-31082989	A549	lung:	n/a
46	chr6:31082939-31082989	HRPEpiC	eye:	n/a
47	chr6:31082939-31082989	HRCEpiC	kidney:	n/a
48	chr6:31082939-31082989	ovcar-3	ovarian:	n/a
49	chr6:31082939-31082989	Hepatocyte	liver:	n/a
50	chr6:31082939-31082989	HAEpiC	amniotic membrane:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31080693..31083957-chr6:31087484..31089976,3	K562	blood:
2	chr6:30852881..30854431-chr6:31082824..31085360,2	MCF-7	breast:
3	chr6:30850897..30852602-chr6:31080609..31083224,2	MCF-7	breast:
4	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:
5	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
6	chr6:31050562..31052756-chr6:31081245..31083912,2	MCF-7	breast:
7	chr6:31082945..31085753-chr6:31086345..31088520,3	MCF-7	breast:

No data

Variant related genes	Relation type
C6orf15	TF binding region
C6orf15	CpG island
ENSG00000137411	Chromatin interaction
ENSG00000204539	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000222895	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11754821	0.96[ASN][1000 genomes]
rs3094216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095300	0.97[EUR][1000 genomes]
rs3130552	0.80[ASN][1000 genomes]
rs3130564	0.86[EUR][1000 genomes]
rs3130976	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130977	0.80[ASN][1000 genomes]
rs3130978	0.80[ASN][1000 genomes]
rs3131006	0.86[EUR][1000 genomes]
rs3132568	0.86[EUR][1000 genomes]
rs41315387	0.94[ASN][1000 genomes]
rs9263580	0.81[ASN][1000 genomes]
rs9263600	0.81[ASN][1000 genomes]
rs9263607	0.81[ASN][1000 genomes]
rs9263623	0.81[ASN][1000 genomes]
rs9263708	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv601490	chr6:31079264-31084435	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv462747	chr6:31082361-31092124	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv601491	chr6:31082361-31092124	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3094220	C6orf1	cis	parietal	SCAN
rs3094220	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3094220	HIST1H3J	cis	parietal	SCAN
rs3094220	CCHCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31080600-31083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:31081000-31083200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31081200-31083200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
5	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
6	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
7	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:31081600-31083000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:31081600-31083200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:31081600-31083400	Enhancers	Brain Cingulate Gyrus	brain
11	chr6:31081600-31083600	Bivalent Enhancer	Placenta	Placenta
12	chr6:31081600-31084000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:31081600-31085400	Enhancers	Lung	lung
14	chr6:31081800-31083200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:31081800-31083200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr6:31081800-31083200	Enhancers	Fetal Muscle Leg	muscle
17	chr6:31081800-31083200	Bivalent Enhancer	Fetal Stomach	stomach
18	chr6:31081800-31083400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:31081800-31083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:31081800-31083400	Enhancers	Left Ventricle	heart
21	chr6:31081800-31084000	Flanking Active TSS	Hela-S3	cervix
22	chr6:31081800-31085400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:31082000-31083000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:31082000-31083200	Bivalent Enhancer	HepG2	liver
25	chr6:31082000-31083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:31082000-31083600	Enhancers	Ovary	ovary
27	chr6:31082200-31083000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr6:31082200-31083000	Flanking Active TSS	NHLF	lung
29	chr6:31082200-31083200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:31082200-31083200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr6:31082200-31083200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:31082200-31083200	Enhancers	Brain Anterior Caudate	brain
33	chr6:31082200-31083200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr6:31082200-31083200	Enhancers	Spleen	Spleen
35	chr6:31082200-31083400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:31082200-31083400	Enhancers	Small Intestine	intestine
37	chr6:31082200-31083400	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr6:31082200-31083600	Flanking Active TSS	NHEK	skin
39	chr6:31082200-31083800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:31082200-31083800	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr6:31082200-31084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:31082200-31084400	Enhancers	Gastric	stomach
43	chr6:31082400-31083000	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:31082400-31083000	Flanking Active TSS	Osteobl	bone
45	chr6:31082400-31083200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:31082400-31083200	Flanking Active TSS	Colonic Mucosa	Colon
47	chr6:31082400-31083200	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:31082400-31083200	Active TSS	A549	lung
49	chr6:31082400-31083400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:31082400-31083400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links