Variant report

Variant	rs1766861
Chromosome Location	chr1:113614839-113614840
allele	C/T
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	CBX3	chr1:113614710-113616713	K562	blood:	n/a	n/a
2	ARID3A	chr1:113614699-113615830	K562	blood:	n/a	n/a
3	ATF1	chr1:113614716-113615966	K562	blood:	n/a	n/a
4	CEBPB	chr1:113614761-113615472	IMR90	lung:	n/a	chr1:113614859-113614870
5	SMARCB1	chr1:113614679-113616267	K562	blood:	n/a	n/a
6	ATF3	chr1:113614669-113615046	K562	blood:	n/a	n/a
7	RCOR1	chr1:113614768-113616833	K562	blood:	n/a	n/a
8	CTCF	chr1:113614616-113616959	SK-N-SH	brain:	n/a	chr1:113615386-113615399 chr1:113615383-113615401
9	CEBPB	chr1:113614725-113615036	K562	blood:	n/a	chr1:113614859-113614870
10	TAL1	chr1:113614718-113616753	K562	blood:	n/a	n/a
11	JUND	chr1:113614780-113616383	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFF	chr1:113614723-113615025	HepG2	liver:	n/a	chr1:113614863-113614881
13	CEBPD	chr1:113614650-113616514	K562	blood:	n/a	n/a
14	CTCF	chr1:113614771-113616621	HCT-116	colon:	n/a	chr1:113615386-113615399 chr1:113615383-113615401
15	ELK1	chr1:113614823-113614905	K562	blood:	n/a	n/a
16	MYC	chr1:113614710-113616768	K562	blood:	n/a	chr1:113614819-113614829 chr1:113616695-113616703 chr1:113616690-113616703
17	ATF3	chr1:113614690-113615028	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:113614798-113616918	K562	blood:	n/a	n/a
19	IRF1	chr1:113614788-113616710	K562	blood:	n/a	chr1:113615772-113615781
20	MAFF	chr1:113614686-113615637	K562	blood:	n/a	chr1:113614863-113614881
21	RAD21	chr1:113614821-113616959	SK-N-SH	brain:	n/a	chr1:113615384-113615403 chr1:113615389-113615399 chr1:113615124-113615133 chr1:113615387-113615400 chr1:113615389-113615401
22	ATF3	chr1:113614687-113615025	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr1:113614702-113616371	Hela-S3	cervix:	n/a	chr1:113614859-113614870 chr1:113615772-113615780
24	HCFC1	chr1:113614756-113616431	K562	blood:	n/a	n/a
25	CTCF	chr1:113614800-113614950	AoAF	blood vessel:	n/a	n/a
26	CEBPB	chr1:113614592-113615855	K562	blood:	n/a	chr1:113614859-113614870 chr1:113615772-113615780
27	MAFK	chr1:113614772-113614999	H1-hESC	embryonic stem cell:	n/a	chr1:113614864-113614879
28	CEBPD	chr1:113614604-113616127	K562	blood:	n/a	n/a
29	NR2F2	chr1:113614657-113616009	K562	blood:	n/a	n/a
30	BHLHE40	chr1:113614776-113616877	K562	blood:	n/a	chr1:113616692-113616701 chr1:113616692-113616701 chr1:113616691-113616700
31	CEBPB	chr1:113614733-113615981	A549	lung:	n/a	chr1:113614859-113614870 chr1:113615772-113615780
32	MAFK	chr1:113614682-113616300	K562	blood:	n/a	chr1:113614864-113614879
33	JUN	chr1:113614768-113616782	K562	blood:	n/a	n/a
34	CTCF	chr1:113614711-113616719	A549	lung:	n/a	chr1:113615386-113615399 chr1:113615383-113615401
35	MYC	chr1:113614773-113616870	K562	blood:	n/a	chr1:113614819-113614829 chr1:113616695-113616703 chr1:113616690-113616703
36	TEAD4	chr1:113614605-113616826	K562	blood:	n/a	n/a
37	GATA1	chr1:113614559-113616125	PBDE	blood:	n/a	n/a
38	ZMIZ1	chr1:113614728-113616384	K562	blood:	n/a	n/a
39	JUND	chr1:113614654-113616425	K562	blood:	n/a	n/a
40	TBL1XR1	chr1:113614709-113616389	K562	blood:	n/a	n/a
41	JUN	chr1:113614096-113617273	K562	blood:	n/a	chr1:113617087-113617097 chr1:113617087-113617097 chr1:113617087-113617097 chr1:113617087-113617097
42	TBP	chr1:113614790-113616500	K562	blood:	n/a	n/a
43	ZC3H11A	chr1:113614726-113616011	K562	blood:	n/a	n/a
44	TBP	chr1:113614766-113616453	H1-hESC	embryonic stem cell:	n/a	n/a
45	CEBPB	chr1:113614587-113615844	K562	blood:	n/a	chr1:113614859-113614870 chr1:113615772-113615780
46	CCNT2	chr1:113614736-113616365	K562	blood:	n/a	n/a
47	ZNF384	chr1:113614815-113616285	K562	blood:	n/a	n/a
48	RCOR1	chr1:113614682-113616779	K562	blood:	n/a	n/a
49	MAX	chr1:113614749-113616497	K562	blood:	n/a	chr1:113614819-113614829
50	POLR2A	chr1:113614787-113616427	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113614064..113616964-chr1:113668302..113669880,2	K562	blood:
2	chr1:113613175..113615596-chr1:113621813..113624852,3	K562	blood:
3	chr1:113493791..113500715-chr1:113613796..113618010,15	K562	blood:
4	chr1:113257532..113261488-chr1:113614794..113617265,4	K562	blood:
5	chr1:113495059..113500488-chr1:113613593..113618010,11	K562	blood:
6	chr1:113610863..113612583-chr1:113613310..113615320,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-2	chr1:113614707-113615830	NONHSAT005314

Variant related genes	Relation type
LRIG2	TF binding region
ENSG00000155380	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000237278	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000226419	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11102594	0.91[YRI][hapmap]
rs1216765	1.00[AMR][1000 genomes]
rs1216788	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs1216789	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs1216794	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216795	0.83[ASW][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216799	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs1216806	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216809	0.83[ASW][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216811	0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1619202	1.00[AMR][1000 genomes]
rs1632505	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs1778021	1.00[AMR][1000 genomes]
rs2788259	1.00[AMR][1000 genomes]
rs2950633	1.00[AMR][1000 genomes]
rs2950637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4839289	0.82[AFR][1000 genomes]
rs7555465	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs946217	0.83[ASW][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
5	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
6	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
7	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv508537	chr1:113590343-113635803	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv437002	chr1:113592588-113658887	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv435694	chr1:113610263-113616294	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	esv3523036	chr1:113610983-113615192	Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv2497412	chr1:113611029-113614851	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113600400-113615000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:113602400-113615000	Weak transcription	Right Atrium	heart
3	chr1:113614200-113615000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:113614200-113615000	Enhancers	Fetal Intestine Small	intestine
5	chr1:113614400-113615000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:113614400-113615000	Enhancers	Fetal Intestine Large	intestine
7	chr1:113614400-113615000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr1:113614400-113615200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:113614600-113615000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:113614600-113615000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:113614600-113615000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:113614600-113615000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:113614600-113615000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:113614600-113615000	Enhancers	Brain Angular Gyrus	brain
15	chr1:113614600-113615200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:113614600-113615200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:113614600-113615200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:113614600-113615200	Enhancers	Primary B cells from cord blood	blood
19	chr1:113614600-113615200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:113614600-113615400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:113614600-113615400	Flanking Active TSS	HepG2	liver
22	chr1:113614800-113615000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr1:113614800-113615000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:113614800-113615000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:113614800-113615000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:113614800-113615000	Enhancers	Primary B cells from peripheral blood	blood
27	chr1:113614800-113615000	Enhancers	Primary T cells from cord blood	blood
28	chr1:113614800-113615000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:113614800-113615000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:113614800-113615000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:113614800-113615000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:113614800-113615000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:113614800-113615000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr1:113614800-113615000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:113614800-113615000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:113614800-113615000	Enhancers	Brain Cingulate Gyrus	brain
37	chr1:113614800-113615000	Active TSS	Brain Germinal Matrix	brain
38	chr1:113614800-113615000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:113614800-113615000	Enhancers	Fetal Brain Male	brain
40	chr1:113614800-113615000	Active TSS	Fetal Lung	lung
41	chr1:113614800-113615000	Enhancers	Fetal Muscle Leg	muscle
42	chr1:113614800-113615000	Enhancers	Fetal Stomach	stomach
43	chr1:113614800-113615000	Enhancers	Pancreas	Pancrea
44	chr1:113614800-113615000	Active TSS	Rectal Smooth Muscle	rectum
45	chr1:113614800-113615000	Enhancers	Thymus	Thymus
46	chr1:113614800-113615000	Enhancers	A549	lung
47	chr1:113614800-113615000	Enhancers	HMEC	breast
48	chr1:113614800-113615000	Enhancers	HUVEC	blood vessel
49	chr1:113614800-113615000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:113614800-113615000	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links