Variant report

Variant	rs34880256
Chromosome Location	chr1:154308089-154308090
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	CTCF	chr1:154307940-154308090	GM12871	blood:	n/a	n/a
2	CTCF	chr1:154307940-154308090	AG09319	gingival:	n/a	n/a
3	CTCF	chr1:154307940-154308090	HepG2	liver:	n/a	n/a
4	CTCF	chr1:154307960-154308110	GM12865	blood:	n/a	n/a
5	CTCF	chr1:154307958-154308118	GM19240	blood:	n/a	n/a
6	CTCF	chr1:154307940-154308090	GM12878	blood:	n/a	n/a
7	RAD21	chr1:154307325-154308111	HCT-116	colon:	n/a	chr1:154307719-154307733 chr1:154307715-154307734
8	CTCF	chr1:154308020-154308170	AG04449	skin:	n/a	n/a
9	CTCF	chr1:154308000-154308150	GM12868	blood:	n/a	n/a
10	CTCF	chr1:154307960-154308110	AG04449	skin:	n/a	n/a
11	CTCF	chr1:154308040-154308190	GM12864	blood:	n/a	n/a
12	CTCF	chr1:154307947-154308108	GM19238	blood:	n/a	n/a
13	CTCF	chr1:154307980-154308130	WI-38	lung:	n/a	n/a
14	CTCF	chr1:154307112-154308212	A549	lung:	n/a	chr1:154307723-154307732 chr1:154307718-154307734 chr1:154307720-154307730 chr1:154307717-154307735 chr1:154307712-154307733
15	CTCF	chr1:154307971-154308096	GM12892	blood:	n/a	n/a
16	CTCF	chr1:154308003-154308110	GM12891	blood:	n/a	n/a
17	CTCF	chr1:154307301-154308255	SK-N-SH	brain:	n/a	chr1:154307723-154307732 chr1:154307718-154307734 chr1:154307720-154307730 chr1:154307717-154307735 chr1:154307712-154307733
18	CTCF	chr1:154307960-154308110	K562	blood:	n/a	n/a
19	CTCF	chr1:154308000-154308150	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154158329..154159389-chr1:154307310..154308142,3	MCF-7	breast:
2	chr1:154306397..154309276-chr1:154322045..154324098,3	MCF-7	breast:
3	chr1:154264672..154266840-chr1:154306843..154308967,2	MCF-7	breast:
4	chr1:154158245..154159342-chr1:154307445..154308150,3	K562	blood:
5	chr1:154296733..154298208-chr1:154306834..154309045,12	MCF-7	breast:
6	chr1:154307761..154310261-chr1:154310334..154313311,3	K562	blood:
7	chr1:154307201..154309234-chr1:154310188..154312854,2	MCF-7	breast:
8	chr1:154249178..154249965-chr1:154307669..154308184,2	K562	blood:
9	chr1:154307733..154310042-chr1:154313433..154315185,2	K562	blood:
10	chr1:154296862..154297663-chr1:154307293..154308165,3	MCF-7	breast:
11	chr1:154192531..154195371-chr1:154305230..154308167,3	MCF-7	breast:
12	chr1:154244424..154245328-chr1:154307214..154308215,5	K562	blood:
13	chr1:154298398..154299500-chr1:154306705..154308264,16	MCF-7	breast:
14	chr1:154299231..154301355-chr1:154306527..154308310,2	K562	blood:
15	chr1:154153078..154156691-chr1:154305231..154310554,8	MCF-7	breast:
16	chr1:154307075..154308806-chr2:174828188..174830288,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-57P	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000238365	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143515	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11265594	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12058332	0.90[EUR][1000 genomes]
rs12063437	0.90[EUR][1000 genomes]
rs12066892	0.90[EUR][1000 genomes]
rs12068128	0.92[EUR][1000 genomes]
rs12729561	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12749618	0.92[EUR][1000 genomes]
rs16865579	0.89[EUR][1000 genomes]
rs1889316	0.89[EUR][1000 genomes]
rs1931299	0.82[ASN][1000 genomes]
rs1948143	0.91[EUR][1000 genomes]
rs28410194	0.89[EUR][1000 genomes]
rs28530583	0.89[EUR][1000 genomes]
rs34065906	0.81[EUR][1000 genomes]
rs34146123	0.81[EUR][1000 genomes]
rs34640592	0.89[ASN][1000 genomes]
rs34749203	0.89[EUR][1000 genomes]
rs34968830	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35091500	0.85[EUR][1000 genomes]
rs35112510	0.87[EUR][1000 genomes]
rs35229198	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35362987	0.89[ASN][1000 genomes]
rs35387092	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35629421	0.89[EUR][1000 genomes]
rs35800693	0.89[ASN][1000 genomes]
rs36029470	0.82[EUR][1000 genomes]
rs3811451	0.89[EUR][1000 genomes]
rs3811452	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3916566	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4304577	0.89[EUR][1000 genomes]
rs4406622	0.88[EUR][1000 genomes]
rs4414034	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4622059	0.90[EUR][1000 genomes]
rs56023096	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56367957	0.89[ASN][1000 genomes]
rs61578738	0.87[ASN][1000 genomes]
rs61803412	0.89[EUR][1000 genomes]
rs61803414	0.89[EUR][1000 genomes]
rs61804488	0.81[EUR][1000 genomes]
rs61804489	0.81[EUR][1000 genomes]
rs6427560	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6427561	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6662855	0.89[EUR][1000 genomes]
rs6662976	0.91[EUR][1000 genomes]
rs6663105	0.88[EUR][1000 genomes]
rs6667225	0.90[EUR][1000 genomes]
rs6672627	0.90[EUR][1000 genomes]
rs6686621	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690468	0.89[EUR][1000 genomes]
rs6701309	0.90[EUR][1000 genomes]
rs68031662	0.90[EUR][1000 genomes]
rs749966	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511806	0.85[EUR][1000 genomes]
rs7518394	0.86[EUR][1000 genomes]
rs7523399	0.90[EUR][1000 genomes]
rs7530735	0.90[EUR][1000 genomes]
rs7530868	0.90[EUR][1000 genomes]
rs7547298	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7552370	0.90[EUR][1000 genomes]
rs9728024	0.84[EUR][1000 genomes]
rs9787014	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301000-154308400	Weak transcription	Fetal Kidney	kidney
2	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
3	chr1:154302200-154312200	Weak transcription	Gastric	stomach
4	chr1:154302200-154312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:154302400-154322400	Strong transcription	Dnd41	blood
7	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:154302600-154309800	Weak transcription	Fetal Brain Male	brain
9	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
11	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:154303000-154313000	Weak transcription	Colonic Mucosa	Colon
16	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:154303200-154312800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
22	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:154303600-154308800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:154303800-154308800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr1:154304000-154322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:154304200-154312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:154304400-154312800	Weak transcription	Esophagus	oesophagus
28	chr1:154304600-154309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:154304800-154309800	Weak transcription	Right Ventricle	heart
30	chr1:154304800-154312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:154304800-154317800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:154305400-154309600	Weak transcription	GM12878-XiMat	blood
33	chr1:154305400-154311600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:154305800-154309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:154305800-154322200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr1:154306000-154309600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr1:154306000-154309800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:154306200-154308200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:154306200-154314200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:154306400-154308200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:154306400-154308800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:154306400-154310800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:154306400-154322400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:154306600-154308200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:154306600-154308200	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr1:154306600-154308200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr1:154306800-154312000	Weak transcription	HSMM	muscle
48	chr1:154307000-154308200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:154307000-154309600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:154307000-154309600	Weak transcription	K562	blood

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