Variant report

Variant	rs2228253
Chromosome Location	chr17:45994044-45994045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45990771..45994045-chr17:45997430..46001241,5	MCF-7	breast:
2	chr17:45978419..45981029-chr17:45992865..45995390,2	MCF-7	breast:
3	chr17:45960015..45962438-chr17:45993771..45995735,2	MCF-7	breast:
4	chr17:45993432..45995637-chr17:46048272..46050209,2	K562	blood:
5	chr17:45993682..45996053-chr17:46022595..46024336,2	MCF-7	breast:
6	chr17:45993823..45996426-chr17:45998099..46000336,2	K562	blood:
7	chr17:45992709..45994396-chr17:45996856..45998957,2	MCF-7	breast:
8	chr17:45991986..45994660-chr17:45998582..46001397,3	K562	blood:
9	chr17:45990204..45992323-chr17:45993152..45994828,2	MCF-7	breast:
10	chr17:45991270..45994231-chr17:46005074..46007219,2	K562	blood:
11	chr17:45993643..45995953-chr17:46019014..46020704,3	MCF-7	breast:
12	chr17:45971250..45975448-chr17:45992732..45995737,5	MCF-7	breast:
13	chr17:45992911..45994770-chr17:46006904..46009157,2	K562	blood:
14	chr17:45991808..45994318-chr17:46045941..46048411,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000263798	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10459927	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11079801	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108833	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1130932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11652185	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11652827	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654010	0.86[JPT][hapmap]
rs11655068	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655352	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11659126	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11870852	0.93[ASN][1000 genomes]
rs12601827	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602494	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs12939739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13353189	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2228251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2325747	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2325751	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs34064155	0.80[ASN][1000 genomes]
rs34593510	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36124074	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3764396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4369725	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793733	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4794261	0.93[ASN][1000 genomes]
rs4794286	0.96[ASN][1000 genomes]
rs6503934	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67194241	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211859	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs72840237	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8066893	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071003	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9895863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903223	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2228253	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2228253	SP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
2	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
3	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
4	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:45980200-46001800	Weak transcription	K562	blood
8	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
11	chr17:45982600-45996200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:45983200-45995200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:45983200-45995200	Weak transcription	HUVEC	blood vessel
16	chr17:45983200-46000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:45983200-46001200	Weak transcription	A549	lung
18	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
19	chr17:45983400-46000600	Weak transcription	NHDF-Ad	bronchial
20	chr17:45984200-46000600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr17:45984600-45994200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr17:45985600-46000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr17:45986000-46000400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:45987000-46000200	Weak transcription	Aorta	Aorta
25	chr17:45987200-45997000	Weak transcription	HepG2	liver
26	chr17:45988400-46000400	Weak transcription	Brain Substantia Nigra	brain
27	chr17:45988400-46000600	Weak transcription	HSMM	muscle
28	chr17:45991800-45994400	Enhancers	HMEC	breast
29	chr17:45991800-45995000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr17:45991800-45995200	Strong transcription	Fetal Intestine Small	intestine
31	chr17:45991800-45996400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:45991800-46000400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr17:45991800-46006400	Strong transcription	Fetal Stomach	stomach
34	chr17:45992000-45994200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:45992000-45994600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr17:45992000-45995200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr17:45992000-45995200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr17:45992000-45995200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:45992000-45995400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr17:45992000-45995400	Strong transcription	Thymus	Thymus
41	chr17:45992000-45996400	Strong transcription	Dnd41	blood
42	chr17:45992200-45995400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr17:45992400-45994600	Strong transcription	Colonic Mucosa	Colon
44	chr17:45992400-45994600	Enhancers	Right Atrium	heart
45	chr17:45992400-45994800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr17:45992400-46008400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr17:45992600-45994200	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr17:45992600-45994200	Enhancers	Ovary	ovary
49	chr17:45992600-45994400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:45992600-45994400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links