Variant report

Variant	rs351728
Chromosome Location	chr6:109549099-109549100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109548764..109550966-chr6:109576791..109578669,2	K562	blood:
2	chr6:109541946..109544521-chr6:109546672..109551149,4	K562	blood:
3	chr6:109547024..109549681-chr6:109557163..109561294,4	K562	blood:
4	chr6:109536259..109539258-chr6:109548268..109550083,2	K562	blood:

Variant related genes	Relation type
ENSG00000243587	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1008084	0.84[CEU][hapmap]
rs11153161	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153168	0.87[CEU][hapmap]
rs11964178	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11966072	0.83[CEU][hapmap]
rs12176068	0.85[EUR][1000 genomes]
rs1260593	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs1260595	0.92[CEU][hapmap]
rs1260596	0.92[CEU][hapmap]
rs1269172	0.86[EUR][1000 genomes]
rs1271693	0.86[ASN][1000 genomes]
rs1271697	0.86[EUR][1000 genomes]
rs13196219	0.83[CEU][hapmap]
rs13196590	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13200047	0.88[CEU][hapmap]
rs13211313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13211944	0.92[ASN][1000 genomes]
rs1341271	0.84[CEU][hapmap]
rs1341272	0.92[CEU][hapmap]
rs171272	0.86[EUR][1000 genomes]
rs1741921	0.85[EUR][1000 genomes]
rs1741923	0.95[ASN][1000 genomes]
rs1741930	0.92[CEU][hapmap]
rs1761608	0.92[CEU][hapmap]
rs1766814	0.86[EUR][1000 genomes]
rs2483913	0.85[EUR][1000 genomes]
rs34774766	0.95[ASN][1000 genomes]
rs351716	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs351717	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs351718	0.95[ASN][1000 genomes]
rs351719	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351722	0.95[ASN][1000 genomes]
rs351723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs351724	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs351725	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs351726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs351727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351731	0.92[ASN][1000 genomes]
rs351732	0.91[ASN][1000 genomes]
rs351735	0.92[ASN][1000 genomes]
rs351736	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs351737	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs351742	0.92[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs351743	0.85[EUR][1000 genomes]
rs351744	0.98[ASN][1000 genomes]
rs351745	0.81[EUR][1000 genomes]
rs351746	0.95[ASN][1000 genomes]
rs351747	0.95[ASN][1000 genomes]
rs351748	0.81[EUR][1000 genomes]
rs351749	0.86[EUR][1000 genomes]
rs351750	0.95[ASN][1000 genomes]
rs351751	0.96[ASN][1000 genomes]
rs351752	0.86[EUR][1000 genomes]
rs351754	0.81[EUR][1000 genomes]
rs351755	0.81[EUR][1000 genomes]
rs351756	0.81[EUR][1000 genomes]
rs353052	0.92[ASN][1000 genomes]
rs368467	0.92[CEU][hapmap]
rs371960	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs377436	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs378447	0.86[EUR][1000 genomes]
rs381565	0.86[EUR][1000 genomes]
rs386696	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs388526	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392820	0.85[EUR][1000 genomes]
rs396000	0.92[CEU][hapmap]
rs396635	0.95[ASN][1000 genomes]
rs398944	0.86[EUR][1000 genomes]
rs399561	0.92[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs408944	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs410449	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs418093	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs419106	0.92[CEU][hapmap]
rs419998	0.85[EUR][1000 genomes]
rs421790	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422113	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs427960	0.92[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs429534	0.95[ASN][1000 genomes]
rs435090	0.82[EUR][1000 genomes]
rs435611	0.86[EUR][1000 genomes]
rs436880	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437779	0.85[EUR][1000 genomes]
rs440849	0.85[EUR][1000 genomes]
rs442405	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs445796	0.85[EUR][1000 genomes]
rs446974	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs448496	0.96[ASN][1000 genomes]
rs449736	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs449850	0.92[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs455839	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs458185	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs458740	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs459956	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs461487	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs463503	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs463916	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs566164	0.83[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs59673	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6568571	0.87[CEU][hapmap]
rs6919423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925339	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7748918	0.84[CEU][hapmap]
rs830552	0.96[ASN][1000 genomes]
rs830553	0.84[EUR][1000 genomes]
rs830554	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs830556	0.96[ASN][1000 genomes]
rs9320278	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9374080	0.84[CEU][hapmap]
rs9374081	0.83[CEU][hapmap]
rs9384701	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9386774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386775	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386796	0.84[CEU][hapmap]
rs9398188	0.86[EUR][1000 genomes]
rs9400272	0.84[CEU][hapmap]
rs9400273	0.83[CEU][hapmap]
rs9480910	0.85[EUR][1000 genomes]
rs9487048	0.83[CEU][hapmap]

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	nsv527657	chr6:109533385-109579675	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs351728	RAB40AL	trans	parietal	SCAN
rs351728	CD164	cis	parietal	SCAN
rs351728	ATG5	cis	cerebellum	SCAN
rs351728	GSTM2P1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109536000-109550800	Weak transcription	HSMMtube	muscle
2	chr6:109546800-109550000	Weak transcription	Placenta	Placenta
3	chr6:109546800-109557800	Weak transcription	Spleen	Spleen
4	chr6:109547000-109553200	Enhancers	Fetal Intestine Small	intestine
5	chr6:109547400-109551200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:109547800-109553000	Enhancers	Stomach Mucosa	stomach
7	chr6:109548400-109550000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:109548400-109550400	Weak transcription	NHEK	skin
9	chr6:109548600-109550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:109548600-109550600	Weak transcription	Psoas Muscle	Psoas
11	chr6:109548800-109551000	Weak transcription	Esophagus	oesophagus
12	chr6:109549000-109549400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:109549000-109550000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:109549000-109551200	Weak transcription	Pancreas	Pancrea

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