Variant report

Variant	rs1595388
Chromosome Location	chr2:113298828-113298829
allele	C/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	SREBP1	chr2:113297940-113301472	GM12878	blood:	n/a	n/a
2	CBX3	chr2:113298818-113300636	K562	blood:	n/a	n/a
3	IRF1	chr2:113298730-113300291	K562	blood:	n/a	chr2:113299911-113299924 chr2:113299913-113299924 chr2:113299912-113299926 chr2:113299911-113299924 chr2:113299910-113299924 chr2:113299911-113299924 chr2:113299911-113299925 chr2:113299912-113299925 chr2:113299911-113299924 chr2:113299915-113299925 chr2:113299914-113299925 chr2:113299912-113299926 chr2:113299913-113299927
4	POLR2A	chr2:113298814-113300390	HUVEC	blood vessel:	n/a	n/a
5	NFIC	chr2:113298630-113300393	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:113298753-113300643	HL-60	blood:	n/a	n/a
7	JUND	chr2:113298529-113301561	SK-N-SH	brain:	n/a	chr2:113299763-113299772 chr2:113299725-113299734 chr2:113300733-113300741 chr2:113300734-113300741 chr2:113300732-113300742
8	CHD1	chr2:113298614-113300713	IMR90	lung:	n/a	n/a
9	POLR2A	chr2:113298819-113300340	GM12891	blood:	n/a	n/a
10	HCFC1	chr2:113298738-113301218	Hela-S3	cervix:	n/a	n/a
11	SPI1	chr2:113298818-113299571	HL-60	blood:	n/a	chr2:113299104-113299117 chr2:113299107-113299116 chr2:113299105-113299118
12	GABPA	chr2:113298734-113300671	HL-60	blood:	n/a	n/a
13	TBP	chr2:113298763-113300233	GM12878	blood:	n/a	n/a
14	GTF3C2	chr2:113298813-113299437	K562	blood:	n/a	n/a
15	POLR2A	chr2:113298778-113301118	GM12878	blood:	n/a	n/a
16	ELF1	chr2:113298795-113300380	GM12878	blood:	n/a	chr2:113299105-113299116 chr2:113299009-113299022
17	TEAD4	chr2:113298721-113300326	K562	blood:	n/a	n/a
18	IRF1	chr2:113298721-113300210	K562	blood:	n/a	chr2:113299911-113299924 chr2:113299913-113299924 chr2:113299912-113299926 chr2:113299911-113299924 chr2:113299910-113299924 chr2:113299911-113299924 chr2:113299911-113299925 chr2:113299912-113299925 chr2:113299911-113299924 chr2:113299915-113299925 chr2:113299914-113299925 chr2:113299912-113299926 chr2:113299913-113299927
19	RPC155	chr2:113298770-113299282	K562	blood:	n/a	n/a
20	POLR2A	chr2:113298729-113300261	U87	brain:	n/a	n/a
21	MTA3	chr2:113298641-113300953	GM12878	blood:	n/a	n/a
22	MXI1	chr2:113298803-113301272	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:113298770-113301098	GM12892	blood:	n/a	n/a
24	EP300	chr2:113298724-113300229	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:113298809-113301210	GM12891	blood:	n/a	n/a
26	BCLAF1	chr2:113298828-113300428	GM12878	blood:	n/a	n/a
27	JUN	chr2:113298473-113301649	K562	blood:	n/a	chr2:113299763-113299772 chr2:113299725-113299734 chr2:113300733-113300741 chr2:113300734-113300741 chr2:113300732-113300742
28	POLR2A	chr2:113298766-113300380	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:113298625-113300234	K562	blood:	n/a	n/a
30	POLR2A	chr2:113298800-113300609	GM12878	blood:	n/a	n/a
31	ZNF384	chr2:113298564-113299529	K562	blood:	n/a	n/a
32	MXI1	chr2:113298346-113301743	SK-N-SH	brain:	n/a	n/a
33	CEBPB	chr2:113298785-113300233	GM12878	blood:	n/a	chr2:113299724-113299732
34	POLR2A	chr2:113298800-113300508	K562	blood:	n/a	n/a
35	ATF3	chr2:113298786-113299158	K562	blood:	n/a	n/a
36	TBP	chr2:113298757-113300392	K562	blood:	n/a	n/a
37	POLR2A	chr2:113298824-113300691	GM12892	blood:	n/a	n/a
38	POLR2A	chr2:113298768-113300261	U87	brain:	n/a	n/a
39	CEBPB	chr2:113298564-113298880	K562	blood:	n/a	chr2:113298741-113298752
40	RUNX3	chr2:113298463-113300597	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:113298802-113300744	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113297646..113299646-chr2:113402192..113403846,2	K562	blood:
2	chr2:113298042..113299646-chr2:113402346..113405215,2	K562	blood:
3	chr2:113297896..113300759-chr2:113319163..113321961,2	K562	blood:
4	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
5	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
6	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
7	chr12:52584189..52586153-chr2:113298687..113301459,2	MCF-7	breast:
8	chr2:113298665..113301106-chr2:113481233..113484131,2	MCF-7	breast:
9	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
10	chr2:113032895..113034868-chr2:113298043..113301369,3	K562	blood:
11	chr2:112811580..112813458-chr2:113297904..113301248,3	K562	blood:
12	chr2:113235916..113241390-chr2:113298151..113302275,12	MCF-7	breast:
13	chr2:113277911..113280966-chr2:113298764..113301565,3	MCF-7	breast:
14	chr2:113298010..113299910-chr2:113402044..113405043,2	MCF-7	breast:
15	chr2:112811382..112813355-chr2:113297904..113301187,3	K562	blood:
16	chr2:113238238..113241697-chr2:113298157..113301092,6	K562	blood:
17	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:
18	chr2:113238895..113243312-chr2:113297571..113302127,8	K562	blood:

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000125611	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000167767	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10153558	0.85[ASN][1000 genomes]
rs10153801	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10864905	0.89[ASN][1000 genomes]
rs11123139	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123140	0.93[ASN][1000 genomes]
rs11123141	0.95[ASN][1000 genomes]
rs11675730	0.98[ASN][1000 genomes]
rs11676962	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677050	0.91[ASN][1000 genomes]
rs11689338	0.93[ASN][1000 genomes]
rs12618629	0.85[ASN][1000 genomes]
rs12618882	0.95[ASN][1000 genomes]
rs13015669	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437673	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437675	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545133	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304555	0.98[ASN][1000 genomes]
rs35832933	0.84[ASN][1000 genomes]
rs3789723	0.95[ASN][1000 genomes]
rs3816140	0.98[ASN][1000 genomes]
rs3816141	0.91[ASN][1000 genomes]
rs3961775	0.98[ASN][1000 genomes]
rs3980067	0.84[ASN][1000 genomes]
rs41278940	0.98[ASN][1000 genomes]
rs41280572	0.91[ASN][1000 genomes]
rs4849072	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849073	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849074	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849075	0.95[ASN][1000 genomes]
rs4849076	0.98[ASN][1000 genomes]
rs56081241	0.89[ASN][1000 genomes]
rs60703755	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7568539	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7578724	0.88[ASN][1000 genomes]
rs7607358	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1595388	TTL	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
2	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
3	chr2:113287000-113299000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:113287000-113299000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:113287200-113299000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:113287600-113299000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:113287800-113299000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:113287800-113299000	Weak transcription	Liver	Liver
9	chr2:113287800-113299400	Weak transcription	Spleen	Spleen
10	chr2:113288000-113299000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:113288200-113299000	Weak transcription	Right Ventricle	heart
12	chr2:113288200-113299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:113288400-113299000	Weak transcription	Placenta	Placenta
14	chr2:113288800-113299000	Weak transcription	Fetal Lung	lung
15	chr2:113288800-113299200	Weak transcription	Esophagus	oesophagus
16	chr2:113288800-113299200	Weak transcription	Gastric	stomach
17	chr2:113289000-113299000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:113289200-113299000	Weak transcription	Fetal Kidney	kidney
19	chr2:113289400-113299000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:113289600-113299000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:113289800-113299000	Weak transcription	NHDF-Ad	bronchial
22	chr2:113289800-113299200	Weak transcription	Ovary	ovary
23	chr2:113290000-113299000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:113290000-113299000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:113290200-113299200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:113290200-113299200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:113290400-113299000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:113290800-113299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:113290800-113299000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:113290800-113299000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:113290800-113299000	Weak transcription	HMEC	breast
32	chr2:113290800-113299000	Weak transcription	NHLF	lung
33	chr2:113291000-113299000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:113291200-113299000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:113291200-113299000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:113291200-113299000	Weak transcription	Adipose Nuclei	Adipose
37	chr2:113291200-113299000	Weak transcription	Lung	lung
38	chr2:113291200-113299000	Weak transcription	HUVEC	blood vessel
39	chr2:113291200-113299000	Weak transcription	NHEK	skin
40	chr2:113291200-113299000	Weak transcription	Osteobl	bone
41	chr2:113291400-113299000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:113291400-113299000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:113291400-113299000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:113291400-113299000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:113291400-113299200	Weak transcription	HSMMtube	muscle
46	chr2:113291600-113299000	Weak transcription	Brain Angular Gyrus	brain
47	chr2:113291600-113299000	Weak transcription	Fetal Stomach	stomach
48	chr2:113291600-113299200	Weak transcription	HSMM	muscle
49	chr2:113292200-113299000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:113298600-113299000	Enhancers	Primary T cells from cord blood	blood

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