Variant report

Variant	rs6744672
Chromosome Location	chr2:211424398-211424399
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	chr2:211423706..211424704-chrX:49040858..49041500,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000012211	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10172081	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191395	0.82[ASN][1000 genomes]
rs10932339	0.89[GIH][hapmap]
rs10932341	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10932342	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10932343	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904031	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472153	0.95[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12475210	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509820	0.87[GIH][hapmap]
rs2012564	0.83[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247029	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247708	0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250976	0.83[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544304	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544305	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2544306	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2544307	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544308	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544310	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544311	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544312	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664229	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2664230	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2664231	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664232	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664233	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664234	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664236	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664237	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2887913	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3914067	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4673538	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5009272	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6749355	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951878	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981024	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6744672	LANCL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211416800-211425800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:211418200-211424400	Genic enhancers	Fetal Intestine Large	intestine
3	chr2:211418600-211443200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:211421200-211424600	Active TSS	Hela-S3	cervix
5	chr2:211421200-211425400	Active TSS	Liver	Liver
6	chr2:211422000-211424600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:211422600-211427800	Weak transcription	Fetal Kidney	kidney
8	chr2:211423000-211426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:211423600-211432600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:211423800-211425400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:211423800-211428600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:211423800-211432600	Weak transcription	H9 Cell Line	embryonic stem cell

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