Variant report

Variant	rs398290
Chromosome Location	chr2:32503526-32503527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32389583..32392652-chr2:32503120..32506003,3	K562	blood:
2	chr2:32389277..32392458-chr2:32500839..32506003,6	K562	blood:
3	chr2:32502844..32505552-chr2:32580260..32584122,5	K562	blood:
4	chr2:32490466..32494039-chr2:32501355..32504337,3	K562	blood:
5	chr2:32503345..32506313-chr2:32507159..32510968,3	MCF-7	breast:
6	chr2:32502844..32506291-chr2:32580260..32584122,8	K562	blood:

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000091106	Chromatin interaction
ENSG00000115760	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10172308	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1033751	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1153121	0.84[CHD][hapmap]
rs1153122	0.88[ASN][1000 genomes]
rs12612824	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs13409142	0.91[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[YRI][hapmap]
rs176415	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2038537	0.93[ASW][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap]
rs376914	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs387780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390480	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	0.85[ASN][1000 genomes]
rs449348	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs455737	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs458628	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952211	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4952255	0.86[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6755811	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805830	0.82[AMR][1000 genomes];1.00[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
rs398290	SLC30A6	cis	cerebellum	SCAN
rs398290	SLC30A6	cis	parietal	SCAN
rs398290	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32502000-32504000	Active TSS	Psoas Muscle	Psoas
2	chr2:32502200-32504000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr2:32502200-32504200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:32502200-32504200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:32502200-32504400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:32502200-32504400	Active TSS	Stomach Smooth Muscle	stomach
7	chr2:32502400-32503800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:32502400-32503800	Active TSS	Fetal Brain Male	brain
9	chr2:32502400-32503800	Active TSS	Placenta Amnion	Placenta Amnion
10	chr2:32502400-32504000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:32502400-32504000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:32502400-32504000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr2:32502400-32504000	Active TSS	Aorta	Aorta
14	chr2:32502400-32504000	Active TSS	Esophagus	oesophagus
15	chr2:32502400-32504000	Active TSS	Fetal Muscle Trunk	muscle
16	chr2:32502400-32504000	Active TSS	Fetal Thymus	thymus
17	chr2:32502400-32504000	Active TSS	Right Ventricle	heart
18	chr2:32502400-32504200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:32502400-32504200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:32502400-32504200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:32502400-32504200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr2:32502400-32504200	Active TSS	Colonic Mucosa	Colon
23	chr2:32502400-32504200	Active TSS	Placenta	Placenta
24	chr2:32502400-32504200	Active TSS	Left Ventricle	heart
25	chr2:32502400-32504200	Active TSS	Ovary	ovary
26	chr2:32502400-32504200	Active TSS	Pancreas	Pancrea
27	chr2:32502400-32504400	Active TSS	Right Atrium	heart
28	chr2:32502600-32503600	Active TSS	Adipose Nuclei	Adipose
29	chr2:32502600-32503600	Active TSS	Liver	Liver
30	chr2:32502600-32503600	Active TSS	Brain Anterior Caudate	brain
31	chr2:32502600-32503800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:32502600-32503800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:32502600-32503800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:32502600-32503800	Active TSS	Small Intestine	intestine
35	chr2:32502600-32503800	Active TSS	Spleen	Spleen
36	chr2:32502600-32504000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr2:32502600-32504000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:32502600-32504000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:32502600-32504000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:32502600-32504000	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr2:32502600-32504000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:32502600-32504000	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr2:32502600-32504000	Active TSS	Brain Substantia Nigra	brain
44	chr2:32502600-32504000	Active TSS	Fetal Muscle Leg	muscle
45	chr2:32502600-32504000	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr2:32502600-32504000	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:32502600-32504000	Bivalent/Poised TSS	HepG2	liver
48	chr2:32502600-32504200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr2:32502600-32504200	Active TSS	Brain Angular Gyrus	brain
50	chr2:32502600-32504200	Active TSS	Brain Cingulate Gyrus	brain

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