Variant report

Variant	rs11124272
Chromosome Location	chr2:32142520-32142521
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32134403..32136134-chr2:32140450..32142713,2	K562	blood:
2	chr2:32142092..32144055-chr2:32147313..32149126,2	MCF-7	breast:
3	chr2:32141829..32144153-chr2:32389157..32391782,2	K562	blood:

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10779914	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11691939	0.85[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs12478134	0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12991444	0.86[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs17011801	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2280968	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2366547	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35196278	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3754835	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3769605	0.85[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs3769611	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs4952203	0.81[TSI][hapmap]
rs4952244	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs61399065	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71446036	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv873777	chr2:32019747-32197123	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11124272	SLC30A6	cis	cerebellum	SCAN
rs11124272	CD5L	trans	cerebellum	SCAN
rs11124272	SLC30A6	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32061600-32172800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:32075800-32170000	Weak transcription	Aorta	Aorta
3	chr2:32086600-32174400	Weak transcription	NHLF	lung
4	chr2:32088000-32157600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:32089400-32160000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:32099600-32193000	Weak transcription	Hela-S3	cervix
7	chr2:32100800-32147800	Weak transcription	Spleen	Spleen
8	chr2:32105400-32146600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:32107200-32167600	Weak transcription	Left Ventricle	heart
10	chr2:32114400-32153800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:32116200-32173000	Weak transcription	HSMMtube	muscle
12	chr2:32116600-32143000	Weak transcription	Colonic Mucosa	Colon
13	chr2:32116800-32144800	Weak transcription	NHEK	skin
14	chr2:32116800-32148000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:32116800-32166200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:32116800-32169400	Weak transcription	Small Intestine	intestine
17	chr2:32116800-32182200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:32117000-32205200	Weak transcription	NH-A	brain
19	chr2:32117400-32144800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:32118000-32145000	Weak transcription	HSMM	muscle
21	chr2:32118600-32170600	Weak transcription	Gastric	stomach
22	chr2:32119200-32181400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:32119800-32144600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:32119800-32144800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:32119800-32146400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:32122600-32146400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:32124000-32144200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:32124000-32146400	Weak transcription	Brain Substantia Nigra	brain
29	chr2:32124400-32146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:32125200-32144800	Weak transcription	Pancreas	Pancrea
31	chr2:32126200-32170400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:32127400-32147000	Weak transcription	Right Ventricle	heart
33	chr2:32127400-32151400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:32127400-32160400	Weak transcription	Thymus	Thymus
35	chr2:32127400-32190200	Weak transcription	Lung	lung
36	chr2:32127600-32144200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:32127600-32144400	Weak transcription	Fetal Lung	lung
38	chr2:32127600-32151200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:32127600-32152200	Weak transcription	Fetal Brain Female	brain
40	chr2:32127600-32156000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:32127600-32165600	Weak transcription	Dnd41	blood
42	chr2:32127800-32144400	Weak transcription	Osteobl	bone
43	chr2:32127800-32144800	Weak transcription	HMEC	breast
44	chr2:32127800-32147000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:32127800-32154600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:32127800-32169800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:32128000-32143400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:32128000-32151000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:32128400-32170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:32128600-32144400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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