Variant report

Variant	rs9844666
Chromosome Location	chr3:135974216-135974217
allele	A/G
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	ELF1	chr3:135974079-135974387	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135967895..135971293-chr3:135973278..135977937,5	MCF-7	breast:
2	chr3:135913308..135916970-chr3:135973705..135976198,3	K562	blood:

Variant related genes	Relation type
PCCB	TF binding region
ENSG00000174579	Chromatin interaction
ENSG00000114054	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12695645	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079205	0.94[GIH][hapmap]
rs13081671	0.91[GIH][hapmap]
rs13082532	1.00[AFR][1000 genomes]
rs13316214	1.00[ASN][1000 genomes]
rs13321721	1.00[ASN][1000 genomes]
rs1393786	0.94[GIH][hapmap]
rs1393787	1.00[ASW][hapmap];0.94[GIH][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes]
rs1604793	1.00[ASN][1000 genomes]
rs17200216	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17298525	1.00[ASN][1000 genomes]
rs17364492	1.00[ASN][1000 genomes]
rs28535121	1.00[ASW][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs28634226	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669017	0.94[GIH][hapmap]
rs28718456	1.00[ASN][1000 genomes]
rs34031772	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34168675	1.00[ASN][1000 genomes]
rs34282798	1.00[ASN][1000 genomes]
rs34324561	0.84[EUR][1000 genomes]
rs34428695	1.00[ASN][1000 genomes]
rs34757183	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs34913797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35320690	0.94[GIH][hapmap]
rs35326900	1.00[ASN][1000 genomes]
rs35352346	0.91[GIH][hapmap]
rs35522825	1.00[ASN][1000 genomes]
rs35837273	0.89[MKK][hapmap]
rs66890203	1.00[ASN][1000 genomes]
rs6768743	1.00[ASN][1000 genomes]
rs6769762	1.00[ASW][hapmap];0.94[GIH][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap]
rs6786582	0.94[GIH][hapmap]
rs6793835	1.00[ASW][hapmap];0.88[GIH][hapmap]
rs6796523	0.96[EUR][1000 genomes]
rs9810051	0.86[EUR][1000 genomes]
rs9810789	1.00[ASN][1000 genomes]
rs9812579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813115	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818056	1.00[ASN][1000 genomes]
rs9818536	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820621	0.86[EUR][1000 genomes]
rs9823373	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs9826454	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832813	0.83[GIH][hapmap];0.92[MEX][hapmap]
rs9837158	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841529	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848926	0.91[GIH][hapmap]
rs9866840	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870825	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872178	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880211	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs9881400	1.00[ASW][hapmap];0.94[GIH][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv933522	chr3:135968919-135981180	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
4	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9844666	PPP2R3A	cis	parietal	SCAN
rs9844666	ERICH1	trans	parietal	SCAN
rs9844666	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970000-135974400	Weak transcription	Ovary	ovary
2	chr3:135970000-135977200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:135970000-135980000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:135970200-135974400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:135970200-135974600	Weak transcription	Left Ventricle	heart
6	chr3:135970200-135975000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:135970200-135979000	Weak transcription	Esophagus	oesophagus
8	chr3:135970200-135980400	Weak transcription	Gastric	stomach
9	chr3:135970200-135984000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:135970400-135974400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:135970400-135974400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:135970400-135974400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:135970400-135974400	Weak transcription	Fetal Lung	lung
15	chr3:135970400-135974600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:135970400-135974800	Weak transcription	Colonic Mucosa	Colon
17	chr3:135970400-135975000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:135970400-135975000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:135970400-135975200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:135970400-135975200	Weak transcription	NH-A	brain
21	chr3:135970400-135975600	Weak transcription	Aorta	Aorta
22	chr3:135970400-135975600	Weak transcription	Brain Germinal Matrix	brain
23	chr3:135970400-135975600	Weak transcription	Lung	lung
24	chr3:135970400-135975800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:135970400-135979000	Weak transcription	HUVEC	blood vessel
26	chr3:135970400-135981600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:135970400-135995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:135970600-135974400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:135970600-135974400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:135970600-135974400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:135970600-135974400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:135970600-135974400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:135970600-135974400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:135970600-135974600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:135970600-135974600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:135970600-135974600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:135970600-135974600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:135970600-135974600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:135970600-135974600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:135970600-135974600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:135970600-135974600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:135970600-135974600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:135970600-135974600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:135970600-135974600	Weak transcription	Osteobl	bone
45	chr3:135970600-135974800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:135970600-135975000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:135970600-135975000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:135970600-135975000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:135970600-135975000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:135970600-135975000	Weak transcription	Psoas Muscle	Psoas

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