Variant report

Variant	rs12094954
Chromosome Location	chr1:151168286-151168287
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	JUND	chr1:151167601-151168291	MCF-7	breast:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
2	RCOR1	chr1:151167042-151168530	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:151166739-151169180	Hela-S3	cervix:	n/a	n/a
4	MAX	chr1:151167606-151168386	MCF-7	breast:	n/a	chr1:151167845-151167854
5	ZNF384	chr1:151168156-151169230	GM12878	blood:	n/a	n/a
6	EGR1	chr1:151167557-151168441	HCT-116	colon:	n/a	chr1:151168005-151168020 chr1:151167977-151167992 chr1:151167986-151167999
7	POLR2A	chr1:151168175-151168399	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr1:151167330-151169342	MCF-7	breast:	n/a	n/a
9	FOSL2	chr1:151167661-151168319	MCF-7	breast:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167956-151167967 chr1:151167954-151167965
10	ZNF384	chr1:151168233-151168458	K562	blood:	n/a	n/a
11	EP300	chr1:151167600-151168342	ECC-1	luminal epithelium:	n/a	chr1:151167955-151167964
12	TCF12	chr1:151167680-151168320	ECC-1	luminal epithelium:	n/a	chr1:151167924-151167932
13	GATA3	chr1:151167532-151168353	A549	lung:	n/a	n/a
14	RPC155	chr1:151167728-151168879	Hela-S3	cervix:	n/a	n/a
15	TEAD4	chr1:151167647-151168294	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:151167673-151168572	Hela-S3	cervix:	n/a	n/a
17	SP1	chr1:151167498-151168464	A549	lung:	n/a	chr1:151167983-151167993
18	GTF3C2	chr1:151166966-151169329	Hela-S3	cervix:	n/a	n/a
19	TCF12	chr1:151167661-151168351	ECC-1	luminal epithelium:	n/a	chr1:151167924-151167932
20	GABPA	chr1:151167512-151168326	MCF-7	breast:	n/a	n/a
21	SETDB1	chr1:151168237-151169026	U2OS	brain:	n/a	n/a
22	TCF12	chr1:151167763-151168621	SK-N-SH	brain:	n/a	chr1:151167924-151167932
23	EGR1	chr1:151167639-151168375	HCT-116	colon:	n/a	chr1:151168005-151168020 chr1:151167977-151167992 chr1:151167986-151167999
24	FOSL1	chr1:151167644-151168455	HCT-116	colon:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167956-151167967 chr1:151167954-151167965
25	POLR2A	chr1:151166415-151169060	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr1:151167611-151169289	A549	lung:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
27	NFIC	chr1:151167482-151168306	ECC-1	luminal epithelium:	n/a	n/a
28	TCF12	chr1:151167702-151169247	SK-N-SH	brain:	n/a	chr1:151167924-151167932
29	EGR1	chr1:151167561-151168352	MCF-7	breast:	n/a	chr1:151168005-151168020 chr1:151167977-151167992 chr1:151167986-151167999
30	SP1	chr1:151167436-151168445	HCT-116	colon:	n/a	chr1:151167983-151167993
31	JUND	chr1:151167641-151168365	MCF-7	breast:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
32	FOSL2	chr1:151167551-151168440	A549	lung:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167956-151167967 chr1:151167954-151167965
33	FOXM1	chr1:151167359-151168357	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:151167673-151169095	Hela-S3	cervix:	n/a	n/a
35	SIN3AK20	chr1:151167573-151168336	MCF-7	breast:	n/a	n/a
36	SIN3AK20	chr1:151167534-151168420	MCF-7	breast:	n/a	n/a
37	TCF12	chr1:151167495-151169258	A549	lung:	n/a	chr1:151167924-151167932

No.	Distal block	Cell Line	Cell type
1	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
2	chr1:151167521..151168494-chr3:149530058..149530684,2	Hela-S3	cervix:
3	chr1:151166423..151168363-chr1:151318010..151319809,2	MCF-7	breast:
4	chr1:151167814..151170369-chr1:151245194..151246986,2	MCF-7	breast:
5	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
6	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
7	chr1:151166432..151169145-chr1:151169439..151172527,5	MCF-7	breast:
8	chr1:151166438..151169666-chr1:151298490..151301352,3	MCF-7	breast:
9	chr1:151164944..151168688-chr1:151252728..151255250,4	MCF-7	breast:
10	chr1:151041779..151043840-chr1:151166772..151169795,3	MCF-7	breast:
11	chr1:151167452..151169662-chr1:151226503..151228827,3	MCF-7	breast:

Variant related genes	Relation type
PIP5K1A	TF binding region
VPS72	TF binding region
ENSG00000237976	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000082996	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143393	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11204788	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11204789	1.00[AMR][1000 genomes]
rs11204790	1.00[AMR][1000 genomes]
rs11204797	1.00[AMR][1000 genomes]
rs11204799	1.00[AMR][1000 genomes]
rs11204800	1.00[AMR][1000 genomes]
rs11204801	1.00[AMR][1000 genomes]
rs11204802	1.00[AMR][1000 genomes]
rs11204804	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12057875	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12058806	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12065050	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068012	0.82[AFR][1000 genomes]
rs12071605	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12073695	1.00[AMR][1000 genomes]
rs12077026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077958	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12080668	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082248	1.00[AMR][1000 genomes]
rs12086389	1.00[AMR][1000 genomes]
rs12087802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089598	0.82[AFR][1000 genomes]
rs12090291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090912	0.82[AFR][1000 genomes]
rs12092749	1.00[AMR][1000 genomes]
rs61751621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6661777	1.00[AMR][1000 genomes]
rs9887870	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151162800-151170200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:151162800-151170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151163000-151170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151163200-151168600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:151163200-151168600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:151163200-151170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:151163200-151170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:151163200-151170400	Weak transcription	Gastric	stomach
9	chr1:151163200-151170400	Weak transcription	Left Ventricle	heart
10	chr1:151163400-151168600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:151163400-151168600	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:151163400-151168600	Weak transcription	Psoas Muscle	Psoas
13	chr1:151163400-151168800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:151163400-151168800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:151163400-151169000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:151163400-151170000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:151163400-151170200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:151163400-151170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:151163400-151170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:151163400-151170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:151163400-151170200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:151163400-151170400	Weak transcription	Primary T cells from cord blood	blood
23	chr1:151163600-151168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:151163600-151170200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:151163600-151170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:151163600-151170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:151163800-151168600	Weak transcription	Dnd41	blood
28	chr1:151163800-151168800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:151163800-151169000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:151163800-151169000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:151166400-151169200	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr1:151166600-151168600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr1:151166600-151169200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:151166800-151170200	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:151167000-151169200	Active TSS	Duodenum Mucosa	Duodenum
36	chr1:151167000-151169600	Active TSS	Placenta	Placenta
37	chr1:151167000-151172000	Active TSS	Colonic Mucosa	Colon
38	chr1:151167200-151168600	Weak transcription	Stomach Mucosa	stomach
39	chr1:151167200-151168800	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr1:151167200-151168800	Active TSS	Hela-S3	cervix
41	chr1:151167200-151169800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:151167400-151169000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:151167400-151169200	Active TSS	A549	lung
44	chr1:151167400-151169600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:151167600-151168600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:151167600-151169000	Enhancers	HSMM	muscle
47	chr1:151167600-151169600	Weak transcription	Esophagus	oesophagus
48	chr1:151167800-151168400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:151167800-151168400	Flanking Active TSS	Osteobl	bone
50	chr1:151167800-151168600	Enhancers	K562	blood

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