Variant report

Variant	rs12305896
Chromosome Location	chr12:50203132-50203133
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr12:50202368-50203544	IMR90	lung:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50202042..50204692-chr12:50235027..50237888,2	K562	blood:
2	chr12:50202054..50204119-chr12:50221111..50223703,2	K562	blood:
3	chr12:50200354..50203165-chr12:50213791..50216673,2	K562	blood:
4	chr12:50202445..50204111-chr12:50220708..50222560,2	MCF-7	breast:
5	chr12:50202887..50205755-chr12:50205906..50208898,2	K562	blood:
6	chr12:50200446..50205468-chr12:50207348..50211696,6	MCF-7	breast:
7	chr12:50202257..50205352-chr12:50220114..50222671,5	MCF-7	breast:
8	chr12:50198514..50201197-chr12:50201542..50204471,2	MCF-7	breast:
9	chr12:50189974..50194712-chr12:50201594..50205995,4	K562	blood:
10	chr12:50201332..50204489-chr12:50235415..50238606,4	MCF-7	breast:
11	chr12:50197457..50199102-chr12:50202144..50204971,2	K562	blood:
12	chr12:50200354..50204251-chr12:50212561..50215291,3	K562	blood:

No data

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000167566	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000258057	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11169158	0.97[ASN][1000 genomes]
rs11169159	0.97[ASN][1000 genomes]
rs12313989	0.97[ASN][1000 genomes]
rs12316892	0.89[ASN][1000 genomes]
rs2603113	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720288	1.00[ASN][1000 genomes]
rs2720289	1.00[ASN][1000 genomes]
rs3741556	0.94[ASN][1000 genomes]
rs67453698	0.85[ASN][1000 genomes]
rs72644870	0.97[ASN][1000 genomes]
rs72644871	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs897055	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
3	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
4	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:50189200-50214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:50192200-50203200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:50192200-50203800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:50193800-50214600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:50195200-50218400	Weak transcription	K562	blood
12	chr12:50195800-50214400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr12:50196200-50204000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:50196800-50203600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:50197600-50205000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:50197600-50220400	Weak transcription	A549	lung
17	chr12:50198600-50203600	Weak transcription	GM12878-XiMat	blood
18	chr12:50199400-50203400	Weak transcription	HUVEC	blood vessel
19	chr12:50199400-50203600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:50199400-50218400	Weak transcription	HMEC	breast
21	chr12:50199600-50205600	Enhancers	Right Atrium	heart
22	chr12:50199600-50205800	Weak transcription	Primary B cells from cord blood	blood
23	chr12:50199600-50214600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:50199600-50214800	Weak transcription	Liver	Liver
25	chr12:50199800-50206200	Enhancers	Fetal Heart	heart
26	chr12:50200000-50209800	Weak transcription	Spleen	Spleen
27	chr12:50200000-50213800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:50200000-50214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:50200000-50214600	Weak transcription	Pancreas	Pancrea
30	chr12:50200000-50216800	Weak transcription	NHEK	skin
31	chr12:50200000-50219400	Weak transcription	Gastric	stomach
32	chr12:50200200-50214800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:50200400-50205600	Enhancers	Left Ventricle	heart
34	chr12:50200400-50214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:50200400-50215000	Weak transcription	Dnd41	blood
36	chr12:50200600-50209600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:50200800-50205600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:50201200-50205600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr12:50201600-50203200	Strong transcription	Thymus	Thymus
40	chr12:50201600-50203400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:50201600-50205000	Enhancers	Placenta	Placenta
42	chr12:50201600-50205200	Enhancers	Right Ventricle	heart
43	chr12:50201600-50205600	Enhancers	Fetal Thymus	thymus
44	chr12:50201800-50203600	Enhancers	Fetal Lung	lung
45	chr12:50201800-50203800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:50201800-50205000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:50201800-50205200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:50201800-50205400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:50201800-50205600	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:50202000-50203200	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links