Variant report

Variant	rs2280968
Chromosome Location	chr2:32290040-32290041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32286352..32290626-chr2:32388602..32393371,12	K562	blood:
2	chr2:32286363..32290764-chr2:32387862..32393371,13	K562	blood:
3	chr2:32288902..32290872-chr2:32375784..32377323,2	MCF-7	breast:
4	chr2:32262818..32267061-chr2:32286978..32290820,6	MCF-7	breast:
5	chr2:32263531..32265848-chr2:32287148..32290470,4	K562	blood:
6	chr2:32233309..32238481-chr2:32286150..32290599,7	MCF-7	breast:
7	chr2:32235889..32238860-chr2:32287017..32290574,4	MCF-7	breast:
8	chr2:32287157..32290220-chr2:32389830..32392599,3	MCF-7	breast:
9	chr2:32262396..32266546-chr2:32286416..32291415,12	K562	blood:
10	chr2:32263267..32267327-chr2:32283931..32290396,13	MCF-7	breast:
11	chr2:32232898..32237970-chr2:32287390..32290443,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000162961	Chromatin interaction
ENSG00000271228	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11124272	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs11678119	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs11691939	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12478134	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12614686	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs12991444	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13006495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13013695	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap]
rs17011801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs177082	1.00[CEU][hapmap]
rs212689	1.00[CEU][hapmap]
rs212736	0.93[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap]
rs212751	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs212754	1.00[CEU][hapmap]
rs212761	0.93[CEU][hapmap];0.92[YRI][hapmap]
rs2294178	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2366547	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34197800	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs35196278	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs375050	1.00[CEU][hapmap]
rs3752916	0.82[CEU][hapmap]
rs3754835	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap]
rs3769602	0.82[CEU][hapmap]
rs3769605	0.85[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3769611	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs385076	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3851310	0.82[CEU][hapmap]
rs410469	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs462878	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs4952203	0.82[GIH][hapmap]
rs56322034	0.81[AFR][1000 genomes]
rs6543648	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6723154	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs6756085	0.81[EUR][1000 genomes]
rs71446036	0.86[AMR][1000 genomes]
rs7556942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562653	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap]
rs7572964	0.82[CEU][hapmap]
rs7574000	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs2280968	NLRC4	cis	lymphoblastoid	seeQTL
rs2280968	SLC30A6	cis	parietal	SCAN
rs2280968	SLC30A6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32287400-32290200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:32287400-32290200	Active TSS	Fetal Intestine Large	intestine
3	chr2:32287400-32290200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr2:32287600-32290200	Active TSS	Fetal Thymus	thymus
5	chr2:32287600-32290200	Active TSS	Right Ventricle	heart
6	chr2:32287800-32290200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:32287800-32290200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:32287800-32290200	Active TSS	GM12878-XiMat	blood
9	chr2:32287800-32290400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:32287800-32290400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:32288000-32290200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:32288000-32290200	Active TSS	Fetal Intestine Small	intestine
13	chr2:32288000-32290400	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:32288000-32290400	Active TSS	HMEC	breast
15	chr2:32289400-32290400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr2:32289400-32290400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:32289400-32290800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:32289400-32290800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr2:32289600-32290200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:32289600-32290200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:32289600-32290200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr2:32289600-32290200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:32289600-32290200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:32289600-32290200	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr2:32289600-32290200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr2:32289600-32290200	Flanking Active TSS	A549	lung
27	chr2:32289600-32290200	Flanking Active TSS	NHEK	skin
28	chr2:32289600-32290400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:32289600-32290400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr2:32289600-32290400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:32289600-32290400	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr2:32289600-32290400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr2:32289600-32291000	Flanking Active TSS	Dnd41	blood
34	chr2:32289600-32291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:32289600-32330800	Weak transcription	Spleen	Spleen
36	chr2:32289800-32290200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:32289800-32290200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:32289800-32290200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr2:32289800-32290200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:32289800-32290200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:32289800-32290200	Weak transcription	Esophagus	oesophagus
42	chr2:32289800-32290200	Weak transcription	Gastric	stomach
43	chr2:32289800-32290200	Weak transcription	Left Ventricle	heart
44	chr2:32289800-32290200	Weak transcription	Lung	lung
45	chr2:32289800-32290200	Weak transcription	Right Atrium	heart
46	chr2:32289800-32290200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:32289800-32290200	Flanking Active TSS	HepG2	liver
48	chr2:32289800-32290200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:32289800-32290200	Active TSS	NH-A	brain
50	chr2:32289800-32290400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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