Variant report

Variant	rs6531227
Chromosome Location	chr2:20503457-20503458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20503251..20505625-chr2:20506483..20510190,4	K562	blood:
2	chr2:20503251..20505156-chr2:20505532..20508254,2	K562	blood:
3	chr2:20503262..20504823-chr2:20520357..20523063,2	MCF-7	breast:
4	chr2:20495005..20497847-chr2:20502307..20504684,2	MCF-7	breast:
5	chr2:20354974..20357549-chr2:20502769..20504637,2	MCF-7	breast:
6	chr2:20501783..20504502-chr2:20645581..20647102,2	MCF-7	breast:
7	chr2:20503412..20505085-chr2:20523282..20524806,2	K562	blood:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000213729	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1043419	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11096656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096657	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2058553	0.92[ASN][1000 genomes]
rs2160071	0.92[ASN][1000 genomes]
rs4465730	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666300	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666379	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666384	0.85[ASN][1000 genomes]
rs4666385	0.88[ASN][1000 genomes]
rs62124605	0.92[ASN][1000 genomes]
rs62124607	0.85[ASN][1000 genomes]
rs6531228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706872	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734686	0.95[CEU][hapmap]
rs6741559	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];1.00[ASN][1000 genomes]
rs719148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596183	0.82[ASN][1000 genomes]
rs7606633	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917904	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs989982	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999153	chr2:20467929-20521954	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1005366	chr2:20478859-20542134	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:20466000-20530400	Strong transcription	Fetal Thymus	thymus
3	chr2:20467000-20522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:20467200-20526200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:20471800-20522600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:20471800-20533800	Strong transcription	Dnd41	blood
7	chr2:20474600-20528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:20475400-20522400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:20476200-20514400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:20476400-20521000	Strong transcription	Fetal Intestine Large	intestine
11	chr2:20476600-20516400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:20476600-20524800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:20476600-20526600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:20476800-20516800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:20478600-20516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:20480400-20515400	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr2:20483200-20520200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:20483400-20505800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:20483400-20514400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:20488200-20516400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:20488400-20513200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:20488400-20516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:20488400-20517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:20489200-20505600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:20489200-20506200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:20489400-20513000	Weak transcription	Stomach Mucosa	stomach
27	chr2:20489400-20517400	Weak transcription	Psoas Muscle	Psoas
28	chr2:20489800-20525800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:20491000-20513400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:20491400-20504000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:20491400-20522600	Strong transcription	HepG2	liver
32	chr2:20491600-20513200	Weak transcription	Brain Angular Gyrus	brain
33	chr2:20491800-20513600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:20491800-20514800	Weak transcription	Gastric	stomach
35	chr2:20492000-20505000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:20492000-20506800	Weak transcription	Right Atrium	heart
37	chr2:20492400-20505600	Weak transcription	Esophagus	oesophagus
38	chr2:20492400-20513200	Weak transcription	Aorta	Aorta
39	chr2:20492400-20525800	Strong transcription	Liver	Liver
40	chr2:20493600-20507200	Weak transcription	HMEC	breast
41	chr2:20494600-20505600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:20495400-20512200	Strong transcription	Primary T cells from cord blood	blood
43	chr2:20495800-20509600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:20496200-20505400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr2:20496200-20513400	Strong transcription	GM12878-XiMat	blood
46	chr2:20496800-20505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:20496800-20516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:20497400-20505600	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:20497400-20505800	Weak transcription	Brain Anterior Caudate	brain
50	chr2:20497400-20516600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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