Variant report

Variant	rs11928577
Chromosome Location	chr3:150170255-150170256
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	POLR2A	chr3:150170228-150173416	K562	blood:	n/a	n/a
2	GATA1	chr3:150168352-150170334	PBDE	blood:	n/a	chr3:150169221-150169228 chr3:150169570-150169580 chr3:150169899-150169909 chr3:150169221-150169228 chr3:150169221-150169228

No.	Distal block	Cell Line	Cell type
1	chr3:150168904..150171899-chr3:150172868..150174513,3	K562	blood:
2	chr3:150168054..150172807-chr3:150173642..150176262,4	MCF-7	breast:
3	chr3:150170167..150172152-chr3:150238313..150240772,2	MCF-7	breast:
4	chr3:150169139..150170858-chr3:150178413..150180525,2	MCF-7	breast:
5	chr3:150128717..150130834-chr3:150168814..150172247,3	MCF-7	breast:

Variant related genes	Relation type
TSC22D2	TF binding region
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10513368	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513369	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513370	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513371	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513372	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513375	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713072	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714034	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11714123	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925759	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11928948	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066114	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067910	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068946	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073230	0.93[ASN][1000 genomes]
rs13076419	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089766	0.87[EUR][1000 genomes]
rs13317818	0.89[ASN][1000 genomes]
rs1376027	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278131	0.86[ASN][1000 genomes]
rs28571974	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587291	0.89[ASN][1000 genomes]
rs2868430	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34106738	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156311	0.93[ASN][1000 genomes]
rs34419133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503712	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34647320	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34983941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35019980	0.87[EUR][1000 genomes]
rs35234277	0.82[ASN][1000 genomes]
rs35598887	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749400	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811719	0.89[ASN][1000 genomes]
rs61734437	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66816665	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67073112	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67100311	0.87[EUR][1000 genomes]
rs6791546	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799106	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799981	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73165716	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73167540	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7614772	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618493	0.89[ASN][1000 genomes]
rs7620193	0.89[ASN][1000 genomes]
rs7621019	0.89[ASN][1000 genomes]
rs7623100	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827736	0.82[ASN][1000 genomes]
rs9844735	0.89[ASN][1000 genomes]
rs9875752	0.89[ASN][1000 genomes]
rs9879140	0.89[ASN][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	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
3	chr3:150134600-150174800	Weak transcription	Dnd41	blood
4	chr3:150135000-150175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:150137200-150176200	Weak transcription	HepG2	liver
6	chr3:150140000-150171800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:150140000-150176200	Weak transcription	Fetal Stomach	stomach
8	chr3:150141400-150175200	Weak transcription	GM12878-XiMat	blood
9	chr3:150144200-150179000	Weak transcription	Aorta	Aorta
10	chr3:150149600-150176000	Weak transcription	Fetal Brain Female	brain
11	chr3:150151400-150171200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:150151400-150171600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:150152200-150171200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:150153000-150175600	Weak transcription	Right Ventricle	heart
15	chr3:150153600-150178200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:150153800-150176000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:150154000-150175800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:150154200-150176000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:150157800-150173000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:150158600-150178200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:150159800-150171600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:150159800-150175600	Weak transcription	Thymus	Thymus
23	chr3:150159800-150176200	Weak transcription	Spleen	Spleen
24	chr3:150160200-150175800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:150160400-150174800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:150160600-150176200	Weak transcription	Esophagus	oesophagus
27	chr3:150160600-150178000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:150160800-150175200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:150160800-150175200	Weak transcription	Fetal Thymus	thymus
30	chr3:150160800-150175800	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:150160800-150176200	Weak transcription	Fetal Kidney	kidney
32	chr3:150160800-150176200	Weak transcription	Gastric	stomach
33	chr3:150161200-150174800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:150162200-150175000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:150162400-150174600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:150162400-150174800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:150165400-150176200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:150165600-150176800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:150165600-150178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:150165600-150187200	Weak transcription	Small Intestine	intestine
41	chr3:150165800-150175000	Weak transcription	Primary B cells from cord blood	blood
42	chr3:150165800-150176200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:150166000-150186200	Weak transcription	Brain Germinal Matrix	brain
44	chr3:150166200-150171200	Weak transcription	Stomach Mucosa	stomach
45	chr3:150166200-150174600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:150166200-150174800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:150166200-150175200	Weak transcription	Left Ventricle	heart
48	chr3:150166400-150171800	Weak transcription	Psoas Muscle	Psoas
49	chr3:150166400-150175200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:150166400-150175200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links