Variant report

Variant	rs6439997
Chromosome Location	chr3:141030065-141030066
allele	A/G
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	chr3:141029730-141030085	U87	brain:	n/a	n/a
2	POLR2A	chr3:141029877-141031261	U87	brain:	n/a	n/a
3	POLR2A	chr3:141029848-141031086	GM18526	blood:	n/a	n/a
4	YY1	chr3:141029886-141030982	GM12892	blood:	n/a	n/a
5	GATA1	chr3:141029608-141033138	K562	blood:	n/a	chr3:141031684-141031693 chr3:141031986-141031996 chr3:141031704-141031714 chr3:141031706-141031723 chr3:141031705-141031714 chr3:141031747-141031755 chr3:141031684-141031691 chr3:141031683-141031693
6	GABPA	chr3:141029843-141031331	MCF-7	breast:	n/a	chr3:141030693-141030700
7	POLR2A	chr3:141029682-141031738	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:141030029-141031068	HCT-116	colon:	n/a	n/a
9	POLR2A	chr3:141029863-141031123	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:141029448-141031315	PFSK-1	brain:	n/a	n/a
11	ELF1	chr3:141030051-141031137	MCF-7	breast:	n/a	n/a
12	ELF1	chr3:141029841-141031076	GM12878	blood:	n/a	n/a
13	RCOR1	chr3:141030025-141030118	K562	blood:	n/a	n/a
14	POLR2A	chr3:141029862-141030984	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:141029165-141031551	GM12891	blood:	n/a	n/a
16	E2F6	chr3:141029735-141031099	K562	blood:	n/a	chr3:141030530-141030541 chr3:141030359-141030366
17	POLR2A	chr3:141029384-141031221	K562	blood:	n/a	n/a
18	POLR2A	chr3:141029345-141031366	GM19193	blood:	n/a	n/a
19	POLR2A	chr3:141029917-141030970	A549	lung:	n/a	n/a
20	POLR2A	chr3:141029238-141032588	K562	blood:	n/a	n/a
21	POLR2A	chr3:141030059-141031331	NB4	blood:	n/a	n/a
22	MAX	chr3:141029995-141031101	A549	lung:	n/a	n/a
23	MAX	chr3:141029834-141031394	A549	lung:	n/a	n/a
24	CREB1	chr3:141029977-141031000	H1-hESC	embryonic stem cell:	n/a	n/a
25	HCFC1	chr3:141029652-141031281	Hela-S3	cervix:	n/a	n/a
26	ELF1	chr3:141029890-141031068	GM12878	blood:	n/a	n/a
27	YY1	chr3:141029939-141031042	K562	blood:	n/a	n/a
28	POLR2A	chr3:141029200-141031801	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:141029466-141031119	Raji	blood:	n/a	n/a
30	BCL3	chr3:141029989-141031254	A549	lung:	n/a	n/a
31	POLR2A	chr3:141029887-141031094	GM12892	blood:	n/a	n/a
32	POLR2A	chr3:141029759-141032733	PBDE	blood:	n/a	n/a
33	POLR2A	chr3:141029839-141031064	ECC-1	luminal epithelium:	n/a	n/a
34	SMARCB1	chr3:141029930-141030991	Hela-S3	cervix:	n/a	chr3:141030635-141030644 chr3:141030605-141030614
35	SMARCC2	chr3:141029910-141030961	Hela-S3	cervix:	n/a	chr3:141030635-141030644 chr3:141030605-141030614
36	POLR2A	chr3:141029887-141031065	GM12891	blood:	n/a	n/a
37	GABPA	chr3:141029986-141031141	A549	lung:	n/a	chr3:141030693-141030700
38	TCF12	chr3:141029839-141031259	A549	lung:	n/a	n/a
39	MXI1	chr3:141029799-141031576	IMR90	lung:	n/a	n/a
40	ZNF143	chr3:141030047-141031049	H1-hESC	embryonic stem cell:	n/a	chr3:141030607-141030616 chr3:141030637-141030646 chr3:141030642-141030657 chr3:141030635-141030653 chr3:141030605-141030623 chr3:141030635-141030644 chr3:141030605-141030614
41	POLR2A	chr3:141029101-141030108	K562	blood:	n/a	n/a
42	RUNX3	chr3:141030055-141031183	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:141029868-141031060	K562	blood:	n/a	n/a
44	ELF1	chr3:141030025-141031225	HCT-116	colon:	n/a	n/a
45	POLR2A	chr3:141030059-141031262	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr3:141029922-141031074	GM12891	blood:	n/a	n/a
47	POLR2A	chr3:141029463-141031649	GM12878	blood:	n/a	n/a
48	RCOR1	chr3:141030044-141031079	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:141029587-141031135	SK-N-SH	brain:	n/a	n/a
50	WRNIP1	chr3:141030051-141031302	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141029221..141032005-chr3:141199464..141200982,2	MCF-7	breast:
2	chr17:57920552..57922129-chr3:141029319..141031208,2	MCF-7	breast:
3	chr3:141021371..141023874-chr3:141028085..141030183,2	K562	blood:
4	chr3:141029860..141032097-chr3:141173989..141175746,3	K562	blood:
5	chr3:141028495..141032567-chr3:141157435..141162053,7	K562	blood:
6	chr3:140950249..140951889-chr3:141027537..141030239,2	MCF-7	breast:
7	chr3:141029007..141031829-chr3:141128539..141131843,4	MCF-7	breast:
8	chr3:140946468..140949037-chr3:141029081..141031629,2	MCF-7	breast:
9	chr3:141028766..141032567-chr3:141157435..141160159,4	K562	blood:
10	chr3:141020173..141025458-chr3:141027736..141031856,6	K562	blood:
11	chr3:141028943..141030664-chr3:141287005..141289345,2	MCF-7	breast:
12	chr3:141023312..141027474-chr3:141027786..141032081,5	MCF-7	breast:
13	chr3:141029632..141032040-chr3:141170273..141172073,2	K562	blood:
14	chr3:140998105..140999651-chr3:141029649..141032061,2	K562	blood:
15	chr3:141027145..141033256-chr3:141085204..141089995,12	K562	blood:
16	chr3:141029377..141033531-chr3:141165560..141167342,4	MCF-7	breast:
17	chr3:141028623..141032743-chr3:141076399..141079995,4	K562	blood:
18	chr3:141029410..141031621-chr3:141132926..141134468,2	K562	blood:
19	chr3:141030009..141033814-chr3:141085690..141089850,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFDP2-11	chr3:141025328-141030534	NONHSAT092424

Variant related genes	Relation type
ENSG00000249540	TF binding region
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000249540	Chromatin interaction
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs955216	0.92[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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr3:141029400-141030200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr3:141029400-141030400	Flanking Active TSS	Dnd41	blood
3	chr3:141029400-141031000	Active TSS	A549	lung
4	chr3:141029600-141030200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:141029600-141030200	Flanking Active TSS	Liver	Liver
6	chr3:141029600-141030200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr3:141029600-141030200	Flanking Active TSS	Hela-S3	cervix
8	chr3:141029600-141030400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:141029600-141030400	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr3:141029600-141030400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:141029600-141030400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:141029600-141030800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr3:141029600-141030800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:141029600-141031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:141029600-141031000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:141029600-141031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:141029600-141031000	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:141029600-141031200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:141029600-141031600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:141029600-141031600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr3:141029800-141030200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:141029800-141030200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:141029800-141030200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:141029800-141030200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:141029800-141030200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:141029800-141030200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:141029800-141030200	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr3:141029800-141030200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:141029800-141030200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr3:141029800-141030200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:141029800-141030200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:141029800-141030200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:141029800-141030200	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr3:141029800-141030200	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr3:141029800-141030200	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr3:141029800-141030200	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr3:141029800-141030200	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr3:141029800-141030200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:141029800-141030200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:141029800-141030200	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr3:141029800-141030200	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr3:141029800-141030200	Flanking Active TSS	Fetal Brain Male	brain
43	chr3:141029800-141030200	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr3:141029800-141030200	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr3:141029800-141030200	Flanking Active TSS	Fetal Lung	lung
46	chr3:141029800-141030200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:141029800-141030200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr3:141029800-141030200	Enhancers	Spleen	Spleen
49	chr3:141029800-141030200	Flanking Active TSS	HMEC	breast
50	chr3:141029800-141030200	Flanking Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links