Variant report

Variant	rs17154175
Chromosome Location	chr11:59559075-59559076
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	NR2F2	chr11:59558975-59559575	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr11:59558925-59559674	MCF-7	breast:	n/a	n/a
3	GATA3	chr11:59558944-59559596	MCF-7	breast:	n/a	n/a
4	MAX	chr11:59559053-59559595	MCF-7	breast:	n/a	chr11:59559564-59559573
5	MAX	chr11:59558992-59559604	MCF-7	breast:	n/a	chr11:59559564-59559573
6	NR2F2	chr11:59558997-59559674	MCF-7	breast:	n/a	n/a
7	GATA3	chr11:59559005-59559556	MCF-7	breast:	n/a	n/a
8	POLR2A	chr11:59558402-59559726	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:59553096..59555024-chr11:59556824..59559677,2	K562	blood:
2	chr11:59522400..59524393-chr11:59558418..59560308,2	MCF-7	breast:
3	chr11:59557627..59559714-chr11:59622962..59625608,2	MCF-7	breast:
4	chr11:59557765..59559673-chr11:59564880..59566549,2	K562	blood:

Variant related genes	Relation type
STX3	TF binding region
ENSG00000166900	Chromatin interaction
ENSG00000254477	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10501380	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1121991	0.92[EUR][1000 genomes]
rs11230020	0.80[EUR][1000 genomes]
rs11230027	0.80[EUR][1000 genomes]
rs11230037	0.88[EUR][1000 genomes]
rs1151063	1.00[EUR][1000 genomes]
rs1151064	1.00[EUR][1000 genomes]
rs11821333	0.96[EUR][1000 genomes]
rs11821465	0.88[EUR][1000 genomes]
rs12272588	0.92[EUR][1000 genomes]
rs12278859	0.88[EUR][1000 genomes]
rs12278910	0.80[EUR][1000 genomes]
rs12280606	0.88[EUR][1000 genomes]
rs12285828	0.90[EUR][1000 genomes]
rs12287975	0.84[EUR][1000 genomes]
rs12289162	0.88[EUR][1000 genomes]
rs12292682	0.92[EUR][1000 genomes]
rs1287111	1.00[EUR][1000 genomes]
rs1287448	0.80[EUR][1000 genomes]
rs1290457	0.96[EUR][1000 genomes]
rs1290459	0.96[EUR][1000 genomes]
rs1299800	0.80[EUR][1000 genomes]
rs17046	0.96[EUR][1000 genomes]
rs17153910	0.80[EUR][1000 genomes]
rs17154029	0.96[EUR][1000 genomes]
rs17154134	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154138	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154146	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154149	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154157	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154165	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154180	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154195	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154200	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154205	0.82[AMR][1000 genomes]
rs17154222	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17154227	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938690	0.88[EUR][1000 genomes]
rs2186597	0.92[EUR][1000 genomes]
rs2447310	0.81[EUR][1000 genomes]
rs2508335	0.81[EUR][1000 genomes]
rs2509274	1.00[EUR][1000 genomes]
rs2509275	0.98[EUR][1000 genomes]
rs2509276	1.00[EUR][1000 genomes]
rs2509279	0.81[EUR][1000 genomes]
rs2509290	0.96[EUR][1000 genomes]
rs2509730	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927182	0.85[EUR][1000 genomes]
rs2927183	0.96[EUR][1000 genomes]
rs2957223	0.96[EUR][1000 genomes]
rs3110322	0.96[EUR][1000 genomes]
rs3132748	0.96[EUR][1000 genomes]
rs34350918	0.88[EUR][1000 genomes]
rs3781792	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781793	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862660	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41384548	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301803	0.92[EUR][1000 genomes]
rs4356243	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393334	0.92[EUR][1000 genomes]
rs4515985	0.92[EUR][1000 genomes]
rs471369	0.81[EUR][1000 genomes]
rs472152	0.81[EUR][1000 genomes]
rs472177	0.96[EUR][1000 genomes]
rs473087	0.96[EUR][1000 genomes]
rs473490	0.80[EUR][1000 genomes]
rs474844	0.96[EUR][1000 genomes]
rs475706	0.96[EUR][1000 genomes]
rs477577	0.81[EUR][1000 genomes]
rs477729	0.81[EUR][1000 genomes]
rs478167	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479264	0.85[EUR][1000 genomes]
rs481893	0.81[EUR][1000 genomes]
rs482355	1.00[EUR][1000 genomes]
rs482356	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484030	0.81[EUR][1000 genomes]
rs484814	0.85[EUR][1000 genomes]
rs484895	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485008	1.00[EUR][1000 genomes]
rs485803	0.81[EUR][1000 genomes]
rs486587	1.00[EUR][1000 genomes]
rs488331	0.80[EUR][1000 genomes]
rs492652	0.96[EUR][1000 genomes]
rs494110	0.81[EUR][1000 genomes]
rs495564	0.80[EUR][1000 genomes]
rs496938	0.81[EUR][1000 genomes]
rs497596	0.85[EUR][1000 genomes]
rs498099	0.81[EUR][1000 genomes]
rs498299	0.81[EUR][1000 genomes]
rs498388	0.96[EUR][1000 genomes]
rs499054	0.81[EUR][1000 genomes]
rs504016	1.00[EUR][1000 genomes]
rs507235	1.00[EUR][1000 genomes]
rs510122	1.00[EUR][1000 genomes]
rs511785	1.00[EUR][1000 genomes]
rs511957	0.96[EUR][1000 genomes]
rs512194	0.92[EUR][1000 genomes]
rs512695	1.00[EUR][1000 genomes]
rs513979	0.81[EUR][1000 genomes]
rs516912	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519605	1.00[EUR][1000 genomes]
rs519873	0.80[EUR][1000 genomes]
rs521330	1.00[EUR][1000 genomes]
rs523016	1.00[EUR][1000 genomes]
rs524102	0.81[EUR][1000 genomes]
rs526672	0.81[EUR][1000 genomes]
rs528525	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529270	1.00[EUR][1000 genomes]
rs532838	0.80[EUR][1000 genomes]
rs533166	0.85[EUR][1000 genomes]
rs536544	0.85[EUR][1000 genomes]
rs536910	0.80[EUR][1000 genomes]
rs537625	0.96[EUR][1000 genomes]
rs538169	0.81[EUR][1000 genomes]
rs540684	0.96[EUR][1000 genomes]
rs549086	0.85[EUR][1000 genomes]
rs550189	0.96[EUR][1000 genomes]
rs550822	0.80[EUR][1000 genomes]
rs552601	0.96[EUR][1000 genomes]
rs553700	0.80[EUR][1000 genomes]
rs554149	0.96[EUR][1000 genomes]
rs554848	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555175	1.00[EUR][1000 genomes]
rs55667192	0.80[EUR][1000 genomes]
rs561029	0.81[EUR][1000 genomes]
rs561604	0.80[EUR][1000 genomes]
rs562657	0.81[EUR][1000 genomes]
rs563267	0.81[EUR][1000 genomes]
rs563276	0.80[EUR][1000 genomes]
rs563800	0.85[EUR][1000 genomes]
rs565983	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567485	1.00[EUR][1000 genomes]
rs567603	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569326	1.00[EUR][1000 genomes]
rs573592	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57529518	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57871852	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs579192	0.96[EUR][1000 genomes]
rs579373	1.00[EUR][1000 genomes]
rs580242	0.96[EUR][1000 genomes]
rs581265	0.81[EUR][1000 genomes]
rs58169611	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58775794	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60009036	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60094706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61636608	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108731	0.81[EUR][1000 genomes]
rs7114773	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117509	0.85[EUR][1000 genomes]
rs7119778	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123969	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7126593	0.92[EUR][1000 genomes]
rs7131059	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73486962	0.88[EUR][1000 genomes]
rs73486971	0.88[EUR][1000 genomes]
rs73486979	0.88[EUR][1000 genomes]
rs73486988	0.92[EUR][1000 genomes]
rs73486997	0.92[EUR][1000 genomes]
rs7933970	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941643	0.96[EUR][1000 genomes]
rs7946152	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947036	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947514	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952024	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8280	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046086	chr11:59520424-59561455	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	13 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59524600-59573800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:59534400-59559600	Weak transcription	Fetal Brain Female	brain
3	chr11:59534600-59571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:59537600-59570400	Weak transcription	Fetal Kidney	kidney
5	chr11:59540800-59559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:59541000-59560000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr11:59541000-59573600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr11:59541800-59559200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:59542200-59571400	Weak transcription	Thymus	Thymus
10	chr11:59543200-59559200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:59544400-59573200	Weak transcription	Psoas Muscle	Psoas
12	chr11:59546000-59560800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:59546400-59568800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:59551400-59572800	Weak transcription	Dnd41	blood
15	chr11:59551600-59573600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:59551600-59576600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:59551600-59577200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:59552000-59573000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:59554200-59563600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:59554200-59565200	Strong transcription	Primary T cells from cord blood	blood
21	chr11:59554200-59565600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:59554200-59565600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:59554400-59565600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr11:59554400-59569000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:59554600-59564800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:59554600-59565200	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr11:59554600-59565800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:59554600-59569000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:59554800-59559200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:59554800-59560400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:59554800-59564400	Strong transcription	Spleen	Spleen
32	chr11:59554800-59565800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:59554800-59568800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:59554800-59576400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:59554800-59576400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:59555000-59560200	Weak transcription	Brain Substantia Nigra	brain
37	chr11:59555000-59566600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:59555000-59567800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:59555000-59573800	Weak transcription	Small Intestine	intestine
40	chr11:59555000-59576800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:59555200-59560200	Weak transcription	A549	lung
42	chr11:59555200-59565800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:59555200-59566000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:59555400-59563800	Strong transcription	Colonic Mucosa	Colon
45	chr11:59555400-59563800	Strong transcription	Ovary	ovary
46	chr11:59555400-59564200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr11:59555400-59565200	Strong transcription	Primary B cells from cord blood	blood
48	chr11:59555400-59565800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr11:59555400-59566000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:59555600-59559600	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links