Variant report

Variant	rs3106196
Chromosome Location	chr6:33382943-33382944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:33382860-33383010	GM12871	blood:	n/a	n/a
2	POLR2A	chr6:33379963-33384071	SK-N-MC	brain:	n/a	n/a
3	CTCF	chr6:33382880-33383030	WERI-Rb-1	eye:	n/a	n/a
4	POLR2A	chr6:33382795-33383152	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:33379970-33384148	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:33380035-33383888	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:33382730-33383124	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:33380137-33384099	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr6:33382716-33383143	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:33382940-33383175	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr6:33382866-33383204	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr6:33382900-33383050	HFF	foreskin:	n/a	n/a
13	CTCF	chr6:33382800-33382950	GM12868	blood:	n/a	n/a
14	POLR2A	chr6:33380085-33387208	IMR90	lung:	n/a	n/a
15	CTCF	chr6:33382840-33382990	HFF-Myc	foreskin:	n/a	n/a
16	POLR2A	chr6:33382706-33383098	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr6:33382253-33383054	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr6:33382840-33382990	NB4	blood:	n/a	n/a
19	POLR2A	chr6:33382763-33383156	GM12878	blood:	n/a	n/a
20	ZMIZ1	chr6:33382866-33382946	K562	blood:	n/a	n/a
21	ZNF263	chr6:33382257-33383098	HEK293-T-REx	kidney:	n/a	n/a
22	POLR2A	chr6:33380060-33386533	K562	blood:	n/a	n/a
23	POLR2A	chr6:33381629-33383398	K562	blood:	n/a	n/a
24	CTCF	chr6:33382880-33383030	HRPEpiC	eye:	n/a	n/a
25	CTCF	chr6:33382860-33383010	RPTEC	kidney:	n/a	n/a
26	POLR2A	chr6:33382675-33383132	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:33382713-33386910	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:33380895-33384143	K562	blood:	n/a	n/a
29	POLR2A	chr6:33380002-33384129	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:33382711-33383191	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr6:33380390-33383943	K562	blood:	n/a	n/a
32	POLR2A	chr6:33382893-33383093	A549	lung:	n/a	n/a
33	POLR2A	chr6:33382680-33383359	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33382580..33384156-chr6:33587956..33590051,2	K562	blood:
3	chr11:57091732..57092432-chr6:33382453..33383005,2	Hela-S3	cervix:
4	chr6:33263818..33265650-chr6:33381990..33383915,2	K562	blood:
5	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
6	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
7	chr6:33381847..33384907-chr6:33420236..33423106,3	MCF-7	breast:
8	chr6:33264150..33266780-chr6:33381466..33383490,2	K562	blood:
9	chr6:33242345..33244145-chr6:33381102..33383050,3	MCF-7	breast:
10	chr6:33248031..33250805-chr6:33381162..33383303,2	MCF-7	breast:
11	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
12	chr6:33381203..33384118-chr6:33546265..33549089,2	K562	blood:
13	chr6:33371627..33375942-chr6:33381284..33387543,6	K562	blood:
14	chr6:33238401..33240913-chr6:33381042..33383923,3	MCF-7	breast:
15	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:

No data

Variant related genes	Relation type
PHF1	TF binding region
SYNGAP1	TF binding region
ENSG00000149115	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000030110	Chromatin interaction
ENSG00000237441	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs172435	0.82[EUR][1000 genomes]
rs1755038	1.00[ASN][1000 genomes]
rs1755040	1.00[ASN][1000 genomes]
rs210131	1.00[ASN][1000 genomes]
rs210153	1.00[ASN][1000 genomes]
rs210190	1.00[ASN][1000 genomes]
rs213198	1.00[ASN][1000 genomes]
rs2941555	1.00[ASN][1000 genomes]
rs3116713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119026	1.00[ASN][1000 genomes]
rs3130013	1.00[ASN][1000 genomes]
rs3130023	1.00[ASN][1000 genomes]
rs3130026	1.00[ASN][1000 genomes]
rs3130104	1.00[ASN][1000 genomes]
rs3130257	1.00[ASN][1000 genomes]
rs3130258	1.00[ASN][1000 genomes]
rs3130273	1.00[ASN][1000 genomes]
rs35700288	1.00[ASN][1000 genomes]
rs36003672	1.00[ASN][1000 genomes]
rs406009	0.81[EUR][1000 genomes]
rs449978	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4713634	1.00[ASN][1000 genomes]
rs6910721	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7762843	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33379600-33384200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33379600-33384400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:33379600-33384400	Weak transcription	Fetal Kidney	kidney
4	chr6:33379600-33384400	Weak transcription	Stomach Mucosa	stomach
5	chr6:33379800-33383200	Genic enhancers	NHDF-Ad	bronchial
6	chr6:33379800-33383600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:33379800-33384200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr6:33379800-33384200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:33379800-33384400	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr6:33380000-33383000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:33380000-33383000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:33380000-33383200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:33380000-33383400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:33380000-33383400	Strong transcription	Fetal Thymus	thymus
15	chr6:33380000-33383600	Genic enhancers	Dnd41	blood
16	chr6:33380000-33383800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:33380000-33384000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:33380000-33384200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:33380000-33384400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:33380000-33384400	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr6:33380000-33384400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:33380000-33384600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
23	chr6:33380200-33383000	Strong transcription	Fetal Muscle Leg	muscle
24	chr6:33380200-33383200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:33380200-33383200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:33380200-33383200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:33380200-33383200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:33380200-33383200	Strong transcription	Brain Hippocampus Middle	brain
29	chr6:33380200-33383200	Strong transcription	Fetal Intestine Large	intestine
30	chr6:33380200-33383200	Strong transcription	HepG2	liver
31	chr6:33380200-33383400	Strong transcription	NHEK	skin
32	chr6:33380200-33383600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:33380200-33383600	Strong transcription	Esophagus	oesophagus
34	chr6:33380200-33383600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr6:33380200-33383600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:33380200-33383600	Strong transcription	Thymus	Thymus
37	chr6:33380200-33383800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:33380200-33383800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:33380200-33383800	Weak transcription	Right Atrium	heart
40	chr6:33380200-33384000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr6:33380200-33384000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:33380200-33384000	Strong transcription	Aorta	Aorta
43	chr6:33380200-33384000	Strong transcription	Brain Substantia Nigra	brain
44	chr6:33380200-33384200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:33380200-33384400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr6:33380200-33384400	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr6:33380200-33384800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:33380200-33384800	Genic enhancers	Spleen	Spleen
49	chr6:33380400-33383200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:33380400-33383200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links