Variant report

Variant	rs3093553
Chromosome Location	chr6:31549556-31549557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31548394-31550903	HL-60	blood:	n/a	n/a
2	POLR2A	chr6:31545797-31549623	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:31539444-31550290	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:31539494-31550471	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:31541889-31550787	GM12878	blood:	n/a	n/a
6	STAT5A	chr6:31549274-31551051	GM12878	blood:	n/a	chr6:31550245-31550257 chr6:31550735-31550747
7	MTA3	chr6:31539044-31550840	GM12878	blood:	n/a	n/a
8	CTCF	chr6:31548421-31549603	A549	lung:	n/a	n/a
9	POLR2A	chr6:31539679-31550540	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:31548517-31549654	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr6:31549469-31550433	GM12891	blood:	n/a	n/a
12	ELF1	chr6:31548352-31549672	GM12878	blood:	n/a	chr6:31549098-31549109 chr6:31549036-31549048
13	POLR2A	chr6:31548586-31549916	HL-60	blood:	n/a	n/a
14	POLR2A	chr6:31539658-31549590	GM19193	blood:	n/a	n/a
15	STAT5A	chr6:31549230-31549582	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:31548459-31550131	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr6:31539653-31550430	GM18505	blood:	n/a	n/a
18	MAZ	chr6:31548348-31549602	IMR90	lung:	n/a	n/a
19	NR2F2	chr6:31548196-31549596	K562	blood:	n/a	n/a
20	RELA	chr6:31549171-31550654	GM19193	blood:	n/a	n/a
21	BCLAF1	chr6:31548365-31549616	GM12878	blood:	n/a	chr6:31549021-31549034
22	CTCF	chr6:31547836-31549680	SK-N-SH	brain:	n/a	n/a
23	PML	chr6:31545381-31550436	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:31549501-31550363	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:31545965-31550350	NB4	blood:	n/a	n/a
26	POLR2A	chr6:31548490-31550134	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr6:31548414-31550020	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr6:31549520-31549670	HAc	cerebellar:	n/a	n/a
29	POLR2A	chr6:31539016-31550879	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:31548531-31550773	Raji	blood:	n/a	n/a
31	CTBP2	chr6:31548605-31549609	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD2	chr6:31548611-31549756	GM12878	blood:	n/a	chr6:31549043-31549053
33	POLR2A	chr6:31549287-31550383	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:31548394-31550285	GM12892	blood:	n/a	n/a
35	POLR2A	chr6:31548364-31549724	GM12878	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31547406..31549936-chr6:31587524..31589325,2	MCF-7	breast:
2	chr6:31546034..31550400-chr6:31586618..31591027,9	K562	blood:
3	chr6:31525235..31529478-chr6:31547066..31550176,3	K562	blood:
4	chr6:31511781..31517209-chr6:31545410..31553496,14	K562	blood:
5	chr6:31514283..31516079-chr6:31548550..31550492,2	MCF-7	breast:
6	chr6:31506860..31511177-chr6:31547154..31549752,6	K562	blood:
7	chr6:31547327..31550393-chr6:31586001..31589795,6	K562	blood:
8	chr6:31545892..31550426-chr6:31586652..31590237,7	MCF-7	breast:
9	chr6:31513299..31516964-chr6:31547293..31550067,4	K562	blood:
10	chr6:31497072..31502351-chr6:31549039..31551366,5	K562	blood:
11	chr6:31549450..31550019-chr6:31564413..31565383,2	NB4	blood:
12	chr6:31465504..31467038-chr6:31547558..31550219,2	K562	blood:
13	chr6:31548503..31550806-chr6:31631619..31633429,4	MCF-7	breast:
14	chr6:31512960..31516876-chr6:31549415..31551752,3	MCF-7	breast:
15	chr6:31547676..31550388-chr6:31631712..31633963,2	K562	blood:
16	chr6:31547247..31549808-chr6:31584423..31586017,2	K562	blood:
17	chr6:31508169..31513281-chr6:31547465..31550370,6	K562	blood:

No data

Variant related genes	Relation type
LST1	TF binding region
ENSG00000204469	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000204516	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3093662	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3093664	0.88[AMR][1000 genomes]
rs3093668	0.83[ASN][1000 genomes]
rs9267502	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
4	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
5	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
6	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
8	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
9	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
10	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
12	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
13	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
14	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 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	chr6:31547600-31549600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
2	chr6:31547800-31550600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:31547800-31551000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:31547800-31551000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr6:31548000-31549600	Active TSS	Brain Angular Gyrus	brain
6	chr6:31548000-31549600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:31548000-31550800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:31548000-31550800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:31548000-31550800	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:31548200-31549600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:31548200-31549600	Active TSS	Colon Smooth Muscle	Colon
12	chr6:31548200-31549800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:31548200-31550000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:31548200-31550000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:31548200-31550200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:31548200-31550200	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:31548200-31550200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:31548200-31550200	Flanking Active TSS	Liver	Liver
19	chr6:31548200-31550200	Active TSS	Small Intestine	intestine
20	chr6:31548200-31550200	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr6:31548200-31550400	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr6:31548200-31550400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr6:31548200-31550600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:31548200-31550600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:31548400-31549600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:31548400-31549600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:31548400-31549600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:31548400-31549600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:31548400-31549600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr6:31548400-31549600	Active TSS	Ovary	ovary
31	chr6:31548400-31549600	Active TSS	HSMMtube	muscle
32	chr6:31548400-31549800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:31548400-31549800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr6:31548400-31549800	Active TSS	Fetal Kidney	kidney
35	chr6:31548400-31549800	Flanking Active TSS	HMEC	breast
36	chr6:31548400-31549800	Active TSS	HSMM	muscle
37	chr6:31548400-31550000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:31548400-31550000	Flanking Bivalent TSS/Enh	Placenta	Placenta
39	chr6:31548400-31550000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr6:31548400-31550200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
41	chr6:31548400-31550400	Active TSS	Primary T cells from cord blood	blood
42	chr6:31548400-31550400	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr6:31548400-31551400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr6:31548600-31549600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:31548600-31549600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:31548600-31549600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:31548600-31549600	Active TSS	Primary T cells fromperipheralblood	blood
48	chr6:31548600-31549600	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:31548600-31549600	Active TSS	Fetal Lung	lung
50	chr6:31548600-31549600	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links