Variant report

Variant	rs2038774
Chromosome Location	chr6:150499889-150499890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150499104..150501184-chr6:150507779..150510819,3	K562	blood:
2	chr6:150491966..150494133-chr6:150498224..150500888,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12204657	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12215988	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1358727	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2038773	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4289668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6905409	0.84[MEX][hapmap]
rs6927415	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9371344	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9371803	0.95[CHB][hapmap]
rs9383711	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9383714	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9384220	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9384225	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397193	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9397722	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9397726	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9479861	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9479881	0.82[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886770	chr6:150395424-150499889	Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2038774	MYCT1	cis	parietal	SCAN
rs2038774	VIP	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150491400-150506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:150491600-150501400	Weak transcription	HMEC	breast
3	chr6:150494400-150501000	Weak transcription	Fetal Brain Female	brain
4	chr6:150497000-150502000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:150497200-150502400	Enhancers	Left Ventricle	heart
6	chr6:150497800-150500800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:150497800-150511000	Weak transcription	NHEK	skin
8	chr6:150498400-150500200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:150498400-150501000	Weak transcription	Right Atrium	heart
10	chr6:150498600-150501400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:150498800-150500000	Weak transcription	K562	blood
12	chr6:150498800-150501400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:150499200-150500000	Flanking Active TSS	Fetal Heart	heart
14	chr6:150499400-150501400	Weak transcription	Esophagus	oesophagus
15	chr6:150499400-150501600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:150499600-150501400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:150499600-150501800	Weak transcription	Psoas Muscle	Psoas
18	chr6:150499600-150503600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:150499600-150504600	Weak transcription	Colonic Mucosa	Colon
20	chr6:150499600-150505200	Weak transcription	Right Ventricle	heart
21	chr6:150499600-150506000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:150499600-150519600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:150499800-150500800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:150499800-150503400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links