Variant report

Variant	rs11568820
Chromosome Location	chr12:48302545-48302546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48300307..48302640-chr12:48305049..48306879,2	MCF-7	breast:
2	chr12:48297014..48299897-chr12:48301878..48303556,2	K562	blood:
3	chr12:48301680..48304083-chr12:48309800..48311806,2	MCF-7	breast:
4	chr12:48291415..48293817-chr12:48302480..48304953,2	K562	blood:
5	chr12:48300486..48303147-chr12:48306990..48309895,2	MCF-7	breast:
6	chr12:48290096..48306593-chr12:48332606..48350271,44	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10747525	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783219	0.83[JPT][hapmap]
rs10783221	0.87[CEU][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs10875695	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10875697	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875701	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875702	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875703	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875704	0.87[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10875706	0.82[EUR][1000 genomes]
rs10875707	0.82[EUR][1000 genomes]
rs10875708	0.87[CEU][hapmap];0.81[CHD][hapmap];0.82[EUR][1000 genomes]
rs10875709	0.82[EUR][1000 genomes]
rs11168307	0.90[EUR][1000 genomes]
rs11168308	0.89[EUR][1000 genomes]
rs11168311	0.85[EUR][1000 genomes]
rs11168314	0.87[CEU][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168315	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs11168316	0.87[CEU][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168318	0.87[CEU][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168320	0.82[EUR][1000 genomes]
rs11829292	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12316950	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4237855	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4254129	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4334089	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4402365	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4411326	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4442605	1.00[CEU][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4454781	1.00[CEU][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760655	0.81[JPT][hapmap]
rs61920870	0.86[EUR][1000 genomes]
rs7132324	0.83[JPT][hapmap]
rs7136534	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7299460	0.83[JPT][hapmap]
rs7300088	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7300301	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7302235	0.89[ASN][1000 genomes]
rs7303966	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7305180	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7308216	0.90[EUR][1000 genomes]
rs7312286	0.86[JPT][hapmap]
rs7965397	0.92[ASN][1000 genomes]
rs7970314	0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7975675	0.81[EUR][1000 genomes]
rs7976091	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11568820	LASS5	cis	parietal	SCAN
rs11568820	C12orf54	cis	lymphoblastoid	seeQTL
rs11568820	RAPGEF3	cis	parietal	SCAN
rs11568820	AQP6	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48299600-48303800	Weak transcription	Adipose Nuclei	Adipose
2	chr12:48299600-48303800	Weak transcription	Small Intestine	intestine
3	chr12:48299600-48304200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:48299800-48303400	Weak transcription	NHEK	skin
5	chr12:48299800-48304000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:48300000-48303200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:48300000-48303600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48300000-48303600	Weak transcription	HMEC	breast
9	chr12:48300000-48307200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr12:48301000-48303800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:48301200-48303600	Enhancers	HepG2	liver
12	chr12:48301600-48304800	Enhancers	Fetal Intestine Small	intestine
13	chr12:48301800-48302800	Enhancers	Colonic Mucosa	Colon
14	chr12:48301800-48304800	Enhancers	Fetal Intestine Large	intestine
15	chr12:48302000-48304200	Weak transcription	HSMMtube	muscle
16	chr12:48302200-48302600	Weak transcription	Placenta	Placenta
17	chr12:48302200-48302600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:48302200-48303600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:48302400-48303400	Weak transcription	Duodenum Mucosa	Duodenum

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