Variant report

Variant	rs390480
Chromosome Location	chr2:32510072-32510073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32508753..32512437-chr2:32515298..32518048,3	K562	blood:
2	chr2:32503345..32506313-chr2:32507159..32510968,3	MCF-7	breast:
3	chr2:32507841..32511322-chr2:32512913..32517224,5	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10172308	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153121	0.92[CHD][hapmap]
rs1153122	0.82[ASN][1000 genomes]
rs12612824	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs13409142	0.91[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs2038537	0.89[CHD][hapmap]
rs376914	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs387780	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs398290	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs427177	0.83[ASN][1000 genomes]
rs449348	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs455737	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs458628	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952211	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4952255	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6755811	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs805830	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv1002120	chr2:32470452-32539443	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1004279	chr2:32470452-32543369	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs390480	SLC30A6	cis	parietal	SCAN
rs390480	SLC30A6	cis	cerebellum	SCAN
rs390480	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32503600-32518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:32503800-32513200	Weak transcription	Small Intestine	intestine
3	chr2:32503800-32513600	Weak transcription	Gastric	stomach
4	chr2:32503800-32520400	Weak transcription	Spleen	Spleen
5	chr2:32504000-32513200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:32504000-32513600	Weak transcription	Psoas Muscle	Psoas
7	chr2:32504000-32515400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:32504000-32516800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:32504000-32516800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:32504000-32516800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:32504000-32520200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:32504000-32520600	Weak transcription	Aorta	Aorta
13	chr2:32504000-32531200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:32504000-32537600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:32504000-32540200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:32504000-32549400	Weak transcription	HSMMtube	muscle
17	chr2:32504200-32513200	Weak transcription	Colonic Mucosa	Colon
18	chr2:32504200-32513200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:32504200-32514000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:32504200-32514000	Weak transcription	Osteobl	bone
21	chr2:32504200-32514600	Weak transcription	Brain Angular Gyrus	brain
22	chr2:32504200-32516800	Weak transcription	HSMM	muscle
23	chr2:32504200-32520000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:32504200-32520200	Weak transcription	Fetal Kidney	kidney
25	chr2:32504200-32520400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:32504200-32524400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:32504400-32514200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:32504400-32514600	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:32504400-32516400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:32504400-32520200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:32504400-32520200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:32504600-32513800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:32504800-32514400	Weak transcription	Hela-S3	cervix
34	chr2:32504800-32537600	Weak transcription	Fetal Brain Male	brain
35	chr2:32505000-32514200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:32505200-32511400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:32505200-32515400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:32505600-32510800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:32505600-32511000	Strong transcription	Placenta	Placenta
40	chr2:32505800-32510200	Strong transcription	Fetal Thymus	thymus
41	chr2:32505800-32510200	Strong transcription	Dnd41	blood
42	chr2:32506000-32510800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:32506000-32511200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:32506000-32512800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:32506200-32511200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:32506400-32510200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:32507000-32510400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:32507000-32510800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:32507000-32511400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:32507400-32512400	Weak transcription	Rectal Mucosa Donor 29	rectum

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