Variant report

Variant	rs2999156
Chromosome Location	chr1:113247127-113247128
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	MAX	chr1:113247075-113247240	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:113247074-113248127	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:113246393-113248209	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:113246913-113248302	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
6	POLR2A	chr1:113246865-113247216	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:113244126-113248331	GM12878	blood:	n/a	n/a
8	MAZ	chr1:113246923-113250658	IMR90	lung:	n/a	chr1:113247387-113247397 chr1:113248122-113248131
9	POLR2A	chr1:113246289-113248630	K562	blood:	n/a	n/a
10	STAT1	chr1:113247041-113247289	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:113245402-113248867	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
13	POLR2A	chr1:113241110-113248218	K562	blood:	n/a	n/a
14	POLR2A	chr1:113247062-113248179	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:113246569-113248289	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
17	POLR2A	chr1:113246263-113248823	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:113242915-113248528	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:113240211-113248533	A549	lung:	n/a	n/a
20	ESR1	chr1:113247124-113247573	ECC-1	luminal epithelium:	n/a	chr1:113247175-113247190 chr1:113247416-113247433
21	JUN	chr1:113247085-113251456	K562	blood:	n/a	chr1:113248123-113248131 chr1:113247586-113247594 chr1:113248122-113248133 chr1:113247484-113247494 chr1:113247584-113247595 chr1:113248449-113248456
22	POLR2A	chr1:113246443-113248182	GM18505	blood:	n/a	n/a
23	STAT5A	chr1:113247115-113249012	GM12878	blood:	n/a	chr1:113247539-113247547
24	ETS1	chr1:113247083-113248130	K562	blood:	n/a	chr1:113247691-113247698 chr1:113247944-113247955 chr1:113247685-113247699
25	POLR2A	chr1:113247017-113248700	HepG2	liver:	n/a	n/a
26	RELA	chr1:113246899-113248168	GM18951	blood:	n/a	n/a
27	POLR2A	chr1:113246974-113248239	GM12891	blood:	n/a	n/a
28	PAX5	chr1:113247031-113247985	GM12878	blood:	n/a	chr1:113247690-113247699
29	SMARCB1	chr1:113247096-113250480	Hela-S3	cervix:	n/a	chr1:113247585-113247594
30	NR2F2	chr1:113247087-113250506	K562	blood:	n/a	n/a
31	POLR2A	chr1:113240375-113248999	K562	blood:	n/a	n/a
32	SMARCC1	chr1:113247047-113250566	Hela-S3	cervix:	n/a	chr1:113247585-113247594
33	EBF1	chr1:113247006-113248156	GM12878	blood:	n/a	chr1:113247701-113247711 chr1:113247701-113247710 chr1:113247700-113247711 chr1:113247701-113247710
34	POLR2A	chr1:113247073-113248357	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:113241165-113248430	GM12891	blood:	n/a	n/a
36	EP300	chr1:113247096-113248319	ECC-1	luminal epithelium:	n/a	chr1:113247691-113247700 chr1:113247687-113247701 chr1:113248148-113248158
37	POLR2A	chr1:113246519-113248726	K562	blood:	n/a	n/a
38	POLR2A	chr1:113246180-113250420	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr1:113246873-113248275	GM19099	blood:	n/a	n/a
40	POLR2A	chr1:113247080-113248097	GM12891	blood:	n/a	n/a
41	POLR2A	chr1:113247015-113250256	IMR90	lung:	n/a	n/a
42	MAX	chr1:113247072-113248763	K562	blood:	n/a	chr1:113247387-113247397 chr1:113248122-113248131 chr1:113247619-113247629
43	MAZ	chr1:113247103-113248313	GM12878	blood:	n/a	chr1:113247387-113247397 chr1:113248122-113248131
44	POLR2A	chr1:113247039-113249062	K562	blood:	n/a	n/a
45	POLR2A	chr1:113246409-113248294	K562	blood:	n/a	n/a
46	MTA3	chr1:113246360-113249177	GM12878	blood:	n/a	n/a
47	NFIC	chr1:113247004-113248182	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:113246963-113250480	HUVEC	blood vessel:	n/a	n/a
49	RUNX3	chr1:113246903-113248367	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:113246214-113248908	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113160723..113165170-chr1:113245654..113250392,12	K562	blood:
3	chr1:113246571..113250786-chr1:113261233..113263716,3	K562	blood:
4	chr1:113244850..113247809-chr17:57917279..57920025,2	MCF-7	breast:
5	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
6	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
7	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
8	chr1:113193696..113195497-chr1:113246337..113249077,2	K562	blood:
9	chr1:113246571..113247384-chr14:58710844..58711538,2	Hela-S3	cervix:
10	chr1:113245734..113247821-chr9:139221192..139223376,2	MCF-7	breast:
11	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:
12	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
13	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
14	chr1:113167944..113171007-chr1:113245720..113249508,3	MCF-7	breast:
15	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
16	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

Variant related genes	Relation type
RHOC	TF binding region
ENSG00000235299	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000160360	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000184599	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10776755	0.89[GIH][hapmap]
rs12046208	0.91[GIH][hapmap]
rs2999154	0.80[GIH][hapmap]
rs4838959	0.89[GIH][hapmap]
rs6537748	0.89[GIH][hapmap]
rs6537749	0.93[GIH][hapmap]
rs937053	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs954679	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2999156	ST7L	cis	Lymphoblastoid	GTEx
rs2999156	VANGL1	cis	cerebellum	SCAN
rs2999156	ATXN7L2	cis	parietal	SCAN
rs2999156	DRAM2	cis	cerebellum	SCAN
rs2999156	ST7L	cis	uninvolved skin	skin_eQTL
rs2999156	ST7L	cis	multi-tissue	Pritchard
rs2999156	ST7L	cis	lymphoblastoid	seeQTL
rs2999156	ST7L	cis	Adipose Subcutaneous	GTEx
rs2999156	C1orf183	cis	parietal	SCAN
rs2999156	ST7L	cis	Thyroid	GTEx
rs2999156	SYCP1	cis	parietal	SCAN
rs2999156	KCNA10	cis	parietal	SCAN
rs2999156	GPR149	trans	cerebellum	SCAN
rs2999156	ST7L	cis	normal skin	skin_eQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:113240400-113247200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:113240600-113247200	Genic enhancers	Placenta	Placenta
4	chr1:113240800-113247200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:113241200-113247200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:113241600-113249200	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:113242000-113248000	Enhancers	Primary B cells from cord blood	blood
8	chr1:113242800-113247200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:113242800-113247800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:113243800-113247200	Weak transcription	Fetal Brain Female	brain
11	chr1:113244000-113247200	Weak transcription	Brain Germinal Matrix	brain
12	chr1:113244200-113247200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:113244200-113247400	Enhancers	Fetal Heart	heart
14	chr1:113244400-113247200	Weak transcription	Primary T cells from cord blood	blood
15	chr1:113244400-113247200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:113244600-113247200	Weak transcription	Ovary	ovary
17	chr1:113245000-113247200	Enhancers	Right Atrium	heart
18	chr1:113245200-113247200	Enhancers	Fetal Thymus	thymus
19	chr1:113245400-113247800	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:113245600-113247200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:113245800-113247200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:113246000-113247200	Enhancers	HepG2	liver
23	chr1:113246200-113247200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:113246200-113247400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:113246400-113247200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:113246400-113247200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:113246400-113247200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:113246400-113247200	Enhancers	Lung	lung
29	chr1:113246400-113247200	Enhancers	Pancreas	Pancrea
30	chr1:113246400-113247200	Transcr. at gene 5' and 3'	K562	blood
31	chr1:113246400-113247200	Enhancers	NHDF-Ad	bronchial
32	chr1:113246400-113247400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr1:113246400-113247400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:113246400-113247400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
35	chr1:113246400-113249000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:113246600-113247200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:113246600-113247200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
38	chr1:113246600-113247200	Enhancers	Aorta	Aorta
39	chr1:113246600-113247200	Enhancers	Fetal Intestine Large	intestine
40	chr1:113246600-113247200	Enhancers	Fetal Kidney	kidney
41	chr1:113246600-113247200	Enhancers	Psoas Muscle	Psoas
42	chr1:113246600-113247200	Enhancers	HSMMtube	muscle
43	chr1:113246600-113247200	Transcr. at gene 5' and 3'	Osteobl	bone
44	chr1:113246600-113247400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:113246600-113247400	Enhancers	Liver	Liver
46	chr1:113246600-113247400	Enhancers	Esophagus	oesophagus
47	chr1:113246600-113247400	Enhancers	Gastric	stomach
48	chr1:113246600-113247400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr1:113246600-113247400	Transcr. at gene 5' and 3'	NHEK	skin
50	chr1:113246600-113247600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links