Variant report

Variant	rs6042197
Chromosome Location	chr20:1404371-1404372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1403838..1406635-chr20:1407133..1408659,2	K562	blood:
2	chr20:1402742..1405514-chr20:1452729..1455276,2	K562	blood:
3	chr20:1397101..1400734-chr20:1402092..1406050,4	K562	blood:
4	chr20:1404065..1404923-chr20:1483919..1484896,2	K562	blood:
5	chr20:1397917..1400734-chr20:1402889..1405956,3	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11087052	0.84[ASN][1000 genomes]
rs1998007	0.81[ASN][1000 genomes]
rs2144542	0.84[ASN][1000 genomes]
rs2144543	0.84[ASN][1000 genomes]
rs2207828	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2207829	0.81[ASN][1000 genomes]
rs2207830	0.87[ASN][1000 genomes]
rs36018423	0.84[ASN][1000 genomes]
rs4813133	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4814231	0.81[ASN][1000 genomes]
rs4814237	0.84[ASN][1000 genomes]
rs4814240	0.84[ASN][1000 genomes]
rs4814243	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814244	0.84[CHB][hapmap];0.88[ASN][1000 genomes]
rs5019244	0.84[ASN][1000 genomes]
rs6033691	0.81[ASN][1000 genomes]
rs6033707	0.81[ASN][1000 genomes]
rs6033715	0.84[ASN][1000 genomes]
rs6033726	0.84[ASN][1000 genomes]
rs6033728	0.84[ASN][1000 genomes]
rs6033729	0.84[ASN][1000 genomes]
rs6033732	0.84[ASN][1000 genomes]
rs6033744	0.84[ASN][1000 genomes]
rs6033753	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042072	0.81[ASN][1000 genomes]
rs6042074	0.81[ASN][1000 genomes]
rs6042091	0.81[ASN][1000 genomes]
rs6042117	0.84[ASN][1000 genomes]
rs6042118	0.84[ASN][1000 genomes]
rs6042131	0.84[ASN][1000 genomes]
rs6042160	0.84[ASN][1000 genomes]
rs6042170	0.84[ASN][1000 genomes]
rs6042172	0.84[ASN][1000 genomes]
rs6042175	0.84[ASN][1000 genomes]
rs6042207	0.84[ASN][1000 genomes]
rs6042208	0.84[ASN][1000 genomes]
rs6042209	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074593	0.81[ASN][1000 genomes]
rs6074623	0.91[ASN][1000 genomes]
rs6079009	0.81[ASN][1000 genomes]
rs6079010	0.81[ASN][1000 genomes]
rs6079012	0.81[ASN][1000 genomes]
rs6079013	0.81[ASN][1000 genomes]
rs6079015	0.81[ASN][1000 genomes]
rs6105079	0.81[ASN][1000 genomes]
rs6105081	0.81[ASN][1000 genomes]
rs6105102	0.84[ASN][1000 genomes]
rs6105110	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs6109825	0.81[ASN][1000 genomes]
rs6109893	0.84[ASN][1000 genomes]
rs6109894	0.84[ASN][1000 genomes]
rs6109912	0.84[ASN][1000 genomes]
rs6134916	0.84[ASN][1000 genomes]
rs6514382	0.81[ASN][1000 genomes]
rs6514383	0.81[ASN][1000 genomes]
rs750424	0.84[ASN][1000 genomes]
rs873523	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926977	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr20:1399800-1404400	Weak transcription	NHLF	lung
2	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr20:1400000-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr20:1400000-1410600	Weak transcription	Osteobl	bone
5	chr20:1401800-1404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:1401800-1404600	Enhancers	Placenta	Placenta
7	chr20:1402800-1405600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:1403200-1404600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:1403200-1404800	Enhancers	Primary T cells from cord blood	blood
10	chr20:1403200-1405600	Enhancers	HMEC	breast
11	chr20:1403200-1406000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:1403200-1406200	Enhancers	NHEK	skin
13	chr20:1403200-1408000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:1403400-1404400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr20:1404000-1404600	Enhancers	Brain Germinal Matrix	brain
16	chr20:1404000-1405200	Enhancers	K562	blood
17	chr20:1404000-1409000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr20:1404200-1404400	Bivalent/Poised TSS	HepG2	liver
19	chr20:1404200-1404800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr20:1404200-1404800	Enhancers	Brain Substantia Nigra	brain
21	chr20:1404200-1404800	Enhancers	Fetal Intestine Large	intestine
22	chr20:1404200-1405000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr20:1404200-1405000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr20:1404200-1405000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr20:1404200-1405000	Enhancers	Brain Anterior Caudate	brain
26	chr20:1404200-1405000	Enhancers	Stomach Mucosa	stomach
27	chr20:1404200-1405200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr20:1404200-1405200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr20:1404200-1405200	Enhancers	Brain Cingulate Gyrus	brain
30	chr20:1404200-1405400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:1404200-1405400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:1404200-1406000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links