Variant report

Variant	rs28614095
Chromosome Location	chr3:113299644-113299645
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	chr3:113299635-113299645	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:113297202..113299908-chr3:113300399..113302111,2	MCF-7	breast:
2	chr3:113297671..113300136-chr3:113323748..113326182,2	K562	blood:
3	chr3:113211553..113213515-chr3:113297928..113300882,2	MCF-7	breast:

Variant related genes	Relation type
SIDT1	TF binding region
ENSG00000072858	Chromatin interaction
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13327031	0.81[EUR][1000 genomes]
rs13353449	0.81[EUR][1000 genomes]
rs2399487	0.81[EUR][1000 genomes]
rs28539944	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4419353	0.81[EUR][1000 genomes]
rs6438154	0.81[EUR][1000 genomes]
rs6779241	0.81[EUR][1000 genomes]
rs6780720	0.81[EUR][1000 genomes]
rs6781507	0.81[EUR][1000 genomes]
rs6797630	1.00[EUR][1000 genomes]
rs6808103	0.81[EUR][1000 genomes]
rs72950893	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72950895	1.00[EUR][1000 genomes]
rs7645188	0.81[EUR][1000 genomes]
rs9810754	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827490	1.00[EUR][1000 genomes]
rs9827772	0.95[EUR][1000 genomes]
rs9829540	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9846529	1.00[EUR][1000 genomes]
rs9860473	0.86[EUR][1000 genomes]
rs9878186	0.81[EUR][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113279200-113300000	Weak transcription	Thymus	Thymus
2	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:113280400-113304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:113280600-113302400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
6	chr3:113281400-113302200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
9	chr3:113286000-113316800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:113287200-113301400	Weak transcription	Fetal Thymus	thymus
11	chr3:113288000-113300000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:113288000-113302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:113294400-113321600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:113294800-113304200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:113296800-113303600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:113296800-113324200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:113297400-113315600	Strong transcription	GM12878-XiMat	blood
18	chr3:113297800-113300800	Strong transcription	Primary B cells from cord blood	blood
19	chr3:113297800-113308000	Strong transcription	Primary T cells from cord blood	blood
20	chr3:113298600-113302400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:113298800-113309400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:113298800-113315200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:113299200-113299800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:113299200-113300800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:113299200-113301000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:113299400-113300400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:113299400-113302600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:113299400-113308000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:113299400-113315400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:113299600-113300200	Enhancers	Brain Germinal Matrix	brain
31	chr3:113299600-113306400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:113299600-113309400	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links