Variant report

Variant	rs61691368
Chromosome Location	chr12:50200524-50200525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr12:50200177-50200552	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr12:50200024-50200678	HEK293-T-REx	kidney:	n/a	chr12:50200376-50200385
3	USF1	chr12:50200309-50200552	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50192057..50194728-chr12:50200116..50202021,2	MCF-7	breast:
2	chr12:50200144..50201863-chr12:50219253..50221982,2	MCF-7	breast:
3	chr12:50200354..50203165-chr12:50213791..50216673,2	K562	blood:
4	chr12:50200446..50205468-chr12:50207348..50211696,6	MCF-7	breast:
5	chr12:50199658..50201645-chr12:50221367..50223834,2	K562	blood:
6	chr12:50200354..50204251-chr12:50212561..50215291,3	K562	blood:
7	chr12:50191850..50193529-chr12:50199593..50201536,2	K562	blood:
8	chr12:50135738..50138027-chr12:50197622..50200585,2	K562	blood:

No data

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000258057	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10875977	1.00[ASN][1000 genomes]
rs11169164	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169165	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169171	1.00[ASN][1000 genomes]
rs12315844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321190	1.00[ASN][1000 genomes]
rs17123990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56751503	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57832845	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137037	1.00[ASN][1000 genomes]
rs7137262	1.00[ASN][1000 genomes]
rs7313739	1.00[ASN][1000 genomes]
rs73309047	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73309054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309064	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309090	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73310907	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968164	1.00[EUR][1000 genomes];1.00[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:118 , 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	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
9	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:50183400-50202600	Strong transcription	NHLF	lung
12	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:50185000-50202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:50185600-50201200	Strong transcription	Fetal Stomach	stomach
15	chr12:50187200-50203000	Strong transcription	Primary T cells from cord blood	blood
16	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:50189200-50214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:50190400-50203000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:50191000-50200600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:50191200-50201800	Strong transcription	HSMM	muscle
21	chr12:50192200-50200600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:50192200-50203200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:50192200-50203800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr12:50193800-50200600	Strong transcription	Brain Cingulate Gyrus	brain
25	chr12:50193800-50214600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:50195200-50218400	Weak transcription	K562	blood
27	chr12:50195600-50202200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:50195800-50202000	Weak transcription	Psoas Muscle	Psoas
29	chr12:50195800-50214400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:50196200-50204000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:50196800-50200600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:50196800-50203600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:50197400-50202200	Weak transcription	Colonic Mucosa	Colon
34	chr12:50197600-50201400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:50197600-50205000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:50197600-50220400	Weak transcription	A549	lung
37	chr12:50197800-50201800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:50198000-50200600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:50198600-50203600	Weak transcription	GM12878-XiMat	blood
40	chr12:50199200-50201600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:50199200-50201800	Weak transcription	Fetal Lung	lung
42	chr12:50199200-50202200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:50199200-50202400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:50199200-50203000	Weak transcription	Aorta	Aorta
45	chr12:50199400-50201600	Weak transcription	Brain Angular Gyrus	brain
46	chr12:50199400-50202200	Weak transcription	NH-A	brain
47	chr12:50199400-50202400	Weak transcription	Esophagus	oesophagus
48	chr12:50199400-50203000	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:50199400-50203000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:50199400-50203400	Weak transcription	HUVEC	blood vessel

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