Variant report

Variant	rs2397221
Chromosome Location	chr6:56251191-56251192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56246077..56248373-chr6:56250654..56253145,3	MCF-7	breast:
2	chr6:56241738..56245167-chr6:56250105..56253808,4	MCF-7	breast:
3	chr6:56249469..56251533-chr6:56299828..56301896,2	MCF-7	breast:
4	chr6:56250438..56252744-chr6:56257720..56260496,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124749	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11751569	1.00[YRI][hapmap]
rs11757910	1.00[YRI][hapmap]
rs11757941	1.00[YRI][hapmap]
rs11758339	1.00[ASW][hapmap]
rs11759493	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs13218268	1.00[YRI][hapmap]
rs2294697	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2397223	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4143828	0.82[YRI][hapmap]
rs4715620	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715630	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs595238	0.90[YRI][hapmap]
rs601783	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603164	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs604857	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs611044	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs619485	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs633348	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs636389	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6459158	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646336	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs649982	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs659697	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6911502	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs6915564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6936834	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741295	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs7762629	0.82[YRI][hapmap]
rs7775847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9296848	0.87[ASW][hapmap]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2397221	TRAM2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56240400-56252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56240600-56252200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:56240600-56252400	Weak transcription	Left Ventricle	heart
4	chr6:56240800-56251200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:56241200-56252400	Weak transcription	Right Ventricle	heart
6	chr6:56244000-56252200	Weak transcription	Placenta	Placenta
7	chr6:56245600-56251600	Weak transcription	Stomach Mucosa	stomach
8	chr6:56245800-56252200	Enhancers	HepG2	liver
9	chr6:56247000-56251600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:56247400-56251600	Weak transcription	Fetal Intestine Large	intestine
11	chr6:56247400-56263600	Weak transcription	Small Intestine	intestine
12	chr6:56247800-56252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:56247800-56252200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:56247800-56252400	Weak transcription	Pancreas	Pancrea
15	chr6:56247800-56252600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:56247800-56252600	Weak transcription	HMEC	breast
17	chr6:56247800-56252600	Weak transcription	NHEK	skin
18	chr6:56249800-56252200	Weak transcription	Psoas Muscle	Psoas
19	chr6:56250000-56251600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:56250000-56252400	Weak transcription	Aorta	Aorta
21	chr6:56250000-56252400	Weak transcription	Gastric	stomach
22	chr6:56250000-56252600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:56250200-56251200	Weak transcription	Hela-S3	cervix
24	chr6:56250200-56253000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:56250600-56251200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:56251000-56251200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:56251000-56253400	Enhancers	Colon Smooth Muscle	Colon

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