Variant report

Variant	rs1133494
Chromosome Location	chr3:150302822-150302823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150300452-150303913	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150295884..150298630-chr3:150301132..150305152,4	K562	blood:
2	chr3:150298264..150303206-chr3:150320117..150322472,5	MCF-7	breast:

Variant related genes	Relation type
SERP1	TF binding region
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13071114	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13097283	0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs14434	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1464517	0.81[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs16862785	0.82[YRI][hapmap]
rs1818788	0.89[ASN][1000 genomes]
rs1915942	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1915943	0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049229	0.94[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090916	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2204112	0.97[EUR][1000 genomes]
rs2204113	0.82[JPT][hapmap]
rs2868946	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2868947	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440683	1.00[ASN][1000 genomes]
rs6440684	0.84[ASN][1000 genomes]
rs6764672	0.87[ASN][1000 genomes]
rs6787881	0.80[AFR][1000 genomes]
rs6790726	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6798173	0.84[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6801796	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7374917	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7433606	0.86[CEU][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs7628889	1.00[ASN][1000 genomes]
rs7631671	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7638500	1.00[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642917	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9289818	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9289820	0.84[ASN][1000 genomes]
rs9289821	0.89[ASN][1000 genomes]
rs954068	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9809820	0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9819287	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820529	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9836797	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842446	0.85[EUR][1000 genomes]
rs9865177	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9871517	0.88[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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1133494	COMMD2	cis	cerebellum	SCAN
rs1133494	TM4SF4	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150265400-150305800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:150265600-150304200	Weak transcription	Fetal Brain Male	brain
3	chr3:150265600-150320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:150265600-150320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:150266000-150304600	Weak transcription	Fetal Heart	heart
6	chr3:150266000-150307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:150268600-150304000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:150274000-150303000	Weak transcription	Pancreas	Pancrea
9	chr3:150277200-150305200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:150278000-150306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:150278200-150304800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:150278400-150306400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:150279400-150303800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:150280000-150304800	Strong transcription	Fetal Thymus	thymus
15	chr3:150280200-150304400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:150280200-150304600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:150280200-150304800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:150280200-150305000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:150280200-150307800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:150281400-150303800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:150283200-150305200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:150286600-150305400	Weak transcription	Colonic Mucosa	Colon
23	chr3:150289600-150303800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:150289800-150303600	Strong transcription	Hela-S3	cervix
25	chr3:150289800-150304000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:150291600-150306200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:150291800-150303000	Strong transcription	Primary B cells from cord blood	blood
28	chr3:150291800-150304000	Strong transcription	Dnd41	blood
29	chr3:150292000-150304800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:150292400-150304000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:150293200-150303800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:150293400-150303800	Strong transcription	Adipose Nuclei	Adipose
33	chr3:150293400-150303800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:150293400-150304800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:150293800-150304000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:150294000-150303800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:150294200-150304000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:150294200-150304400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:150294200-150305000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:150294200-150314600	Weak transcription	Psoas Muscle	Psoas
41	chr3:150294400-150306600	Weak transcription	Brain Angular Gyrus	brain
42	chr3:150295000-150303200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:150295200-150306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:150295400-150307200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:150295600-150318600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:150296200-150303800	Strong transcription	Placenta	Placenta
47	chr3:150296400-150303800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:150296400-150303800	Strong transcription	Osteobl	bone
49	chr3:150297400-150303800	Strong transcription	Fetal Intestine Large	intestine
50	chr3:150297400-150306400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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