Variant report

Variant	rs1124999
Chromosome Location	chr6:26287043-26287044
allele	G/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	chr6:26286506-26287202	K562	blood:	n/a	n/a
2	REST	chr6:26284969-26287157	H1-neurons	neurons:	n/a	n/a
3	TRIM28	chr6:26284500-26287080	K562	blood:	n/a	n/a
4	JUND	chr6:26284369-26287104	SK-N-SH	brain:	n/a	chr6:26285885-26285894
5	ATF3	chr6:26285280-26287145	A549	lung:	n/a	chr6:26285883-26285893 chr6:26285883-26285896 chr6:26285886-26285896 chr6:26285884-26285895 chr6:26285885-26285893 chr6:26285882-26285897 chr6:26285882-26285893 chr6:26285883-26285894 chr6:26285886-26285893 chr6:26285874-26285894 chr6:26285886-26285897 chr6:26285883-26285896 chr6:26285886-26285894 chr6:26285884-26285895
6	JUN	chr6:26283102-26287746	K562	blood:	n/a	chr6:26285885-26285894 chr6:26285881-26285894
7	ATF3	chr6:26286441-26287047	HCT-116	colon:	n/a	n/a
8	TEAD4	chr6:26286380-26287112	SK-N-SH	brain:	n/a	n/a
9	EP300	chr6:26286919-26287060	K562	blood:	n/a	n/a
10	TEAD4	chr6:26286452-26287045	ECC-1	luminal epithelium:	n/a	n/a
11	CREB1	chr6:26284593-26287131	K562	blood:	n/a	chr6:26285883-26285896
12	SIX5	chr6:26286492-26287167	A549	lung:	n/a	chr6:26286979-26286993
13	CEBPB	chr6:26284776-26287129	GM12878	blood:	n/a	n/a
14	STAT1	chr6:26285339-26287351	Hela-S3	cervix:	n/a	chr6:26286961-26286970 chr6:26286962-26286971 chr6:26286959-26286973 chr6:26286956-26286976 chr6:26286962-26286970 chr6:26286956-26286976
15	MYBL2	chr6:26285188-26287174	HepG2	liver:	n/a	n/a
16	SP1	chr6:26286460-26287073	A549	lung:	n/a	n/a
17	ATF3	chr6:26286457-26287096	HCT-116	colon:	n/a	n/a
18	ATF3	chr6:26286412-26287067	K562	blood:	n/a	n/a
19	MYBL2	chr6:26284953-26287090	HepG2	liver:	n/a	n/a
20	MTA3	chr6:26284024-26287103	GM12878	blood:	n/a	n/a
21	GTF3C2	chr6:26286538-26287127	Hela-S3	cervix:	n/a	n/a
22	IRF4	chr6:26286487-26287063	GM12878	blood:	n/a	n/a
23	GTF3C2	chr6:26286630-26287094	K562	blood:	n/a	n/a
24	PBX3	chr6:26286925-26287140	GM12878	blood:	n/a	n/a
25	ATF3	chr6:26286427-26287103	A549	lung:	n/a	n/a
26	HEY1	chr6:26281617-26287140	K562	blood:	n/a	chr6:26284853-26284868 chr6:26285884-26285893 chr6:26285886-26285895
27	SREBP2	chr6:26284276-26287755	GM12878	blood:	n/a	n/a
28	NR2F2	chr6:26284348-26287068	K562	blood:	n/a	n/a
29	POLR2A	chr6:26280425-26287127	H1-hESC	embryonic stem cell:	n/a	n/a
30	FOSL2	chr6:26286463-26287053	SK-N-SH	brain:	n/a	n/a
31	CUX1	chr6:26286565-26287106	K562	blood:	n/a	chr6:26287033-26287042
32	MAZ	chr6:26284567-26287088	IMR90	lung:	n/a	n/a
33	NFIC	chr6:26284477-26287056	GM12878	blood:	n/a	n/a
34	TEAD4	chr6:26286355-26287046	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26285383..26287322-chr6:26595667..26597252,2	K562	blood:
2	chr6:26285546..26288000-chr6:26593708..26598025,4	K562	blood:
3	chr22:37594612..37596195-chr6:26285298..26287282,2	MCF-7	breast:
4	chr6:26284169..26287182-chr6:27098843..27102282,9	MCF-7	breast:
5	chr6:26282374..26290542-chr6:27772727..27779446,9	MCF-7	breast:
6	chr6:26284926..26288844-chr6:27112544..27117256,7	MCF-7	breast:
7	chr6:26283553..26288411-chr6:27099109..27103890,9	K562	blood:
8	chr6:26283501..26289776-chr6:27108470..27116413,14	K562	blood:
9	chr6:26285889..26287811-chr6:26576369..26578960,2	K562	blood:
10	chr17:50443509..50445009-chr6:26285795..26287525,2	K562	blood:
11	chr6:26286019..26289232-chr6:26328153..26331757,3	MCF-7	breast:
12	chr6:26286125..26287830-chr6:27780556..27782142,2	K562	blood:
13	chr6:26285002..26288145-chr6:27106372..27109970,3	K562	blood:
14	chr17:41380482..41382083-chr6:26284329..26287201,2	MCF-7	breast:
15	chr6:26283553..26287733-chr6:27097522..27103890,12	K562	blood:
16	chr6:26285002..26287189-chr6:27105491..27107872,2	K562	blood:
17	chr6:26280754..26288136-chr6:27109918..27116629,16	MCF-7	breast:
18	chr6:26020607..26022712-chr6:26286327..26288134,2	MCF-7	breast:

Variant related genes	Relation type
HIST1H4H	TF binding region
ENSG00000196176	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000236383	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000133466	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000185130	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1125000	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11756673	0.81[ASN][1000 genomes]
rs12526215	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2142703	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179152	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2393592	0.96[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2393593	0.92[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34916901	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35310879	0.85[EUR][1000 genomes]
rs3999544	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4145910	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4412192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456712	0.85[EUR][1000 genomes]
rs6916289	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6931391	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6939048	0.81[ASN][1000 genomes]
rs6939589	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6940237	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7450556	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs766406	1.00[JPT][hapmap]
rs766407	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7746807	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747133	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748935	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761298	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7769028	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7771202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357004	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358915	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358917	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358919	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366649	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9366651	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9379838	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9379843	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393692	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs9393693	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393694	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461242	0.81[ASN][1000 genomes]
rs9467703	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9467704	0.91[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs989134	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
8	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
9	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
10	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
11	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1124999	HIST1H3I	cis	parietal	SCAN
rs1124999	BTN3A3	cis	lymphoblastoid	seeQTL
rs1124999	ACOT13	cis	cerebellum	SCAN
rs1124999	HIST1H2BK	cis	parietal	SCAN
rs1124999	HIST1H3H	cis	parietal	SCAN
rs1124999	HIST1H4F	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26282800-26287200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:26283400-26287200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:26283400-26287200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:26283400-26287200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:26283600-26287200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:26283600-26287200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:26283600-26287200	Active TSS	Thymus	Thymus
8	chr6:26283800-26287200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:26283800-26287200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:26284000-26287200	Active TSS	Rectal Smooth Muscle	rectum
11	chr6:26284000-26287200	Active TSS	A549	lung
12	chr6:26284200-26287200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:26284200-26287200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:26284400-26287200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:26284600-26287200	Active TSS	Psoas Muscle	Psoas
16	chr6:26285000-26287200	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:26285600-26287200	Active TSS	Osteobl	bone
18	chr6:26285600-26287600	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr6:26286600-26287200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:26286600-26287200	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr6:26286800-26287200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:26286800-26287200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:26286800-26287200	Active TSS	Brain Germinal Matrix	brain
24	chr6:26286800-26287200	Enhancers	Stomach Mucosa	stomach
25	chr6:26286800-26287400	Enhancers	Fetal Intestine Small	intestine
26	chr6:26286800-26287400	Flanking Active TSS	Dnd41	blood
27	chr6:26286800-26287400	Flanking Active TSS	Hela-S3	cervix
28	chr6:26286800-26287800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:26286800-26288400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:26286800-26290400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:26286800-26292200	Weak transcription	Ovary	ovary
32	chr6:26286800-26294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:26286800-26295400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:26287000-26287200	Enhancers	Fetal Stomach	stomach
35	chr6:26287000-26287200	Flanking Active TSS	GM12878-XiMat	blood
36	chr6:26287000-26287200	Flanking Active TSS	HepG2	liver
37	chr6:26287000-26287400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:26287000-26287600	Transcr. at gene 5' and 3'	K562	blood
39	chr6:26287000-26291600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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