Variant report

Variant	rs9826729
Chromosome Location	chr3:150141584-150141585
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150121790..150130149-chr3:150138506..150143439,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10513373	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs10513374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719977	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12638309	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639090	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs13081231	0.99[ASN][1000 genomes]
rs13082720	0.80[ASN][1000 genomes]
rs13099758	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13321876	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450335	0.80[ASN][1000 genomes]
rs1450336	0.80[ASN][1000 genomes]
rs1450344	0.81[JPT][hapmap]
rs16862627	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs16862644	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs16862676	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1868672	0.90[JPT][hapmap]
rs1868673	0.81[JPT][hapmap]
rs28514580	0.80[ASN][1000 genomes]
rs2868425	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4423794	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4681203	0.99[ASN][1000 genomes]
rs4681204	0.84[ASN][1000 genomes]
rs4681205	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4681206	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681207	0.84[ASN][1000 genomes]
rs4681615	0.80[ASN][1000 genomes]
rs4681616	0.84[ASN][1000 genomes]
rs4681617	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs4681618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58628422	0.99[ASN][1000 genomes]
rs67319423	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762432	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6770424	0.91[JPT][hapmap]
rs6784048	0.99[ASN][1000 genomes]
rs6792734	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792759	0.81[JPT][hapmap]
rs6795124	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6810143	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs73165707	0.84[ASN][1000 genomes]
rs7427177	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7626725	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651353	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651989	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9289809	0.81[CEU][hapmap]
rs9289810	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs9784335	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813752	0.80[ASN][1000 genomes]
rs9846873	0.81[ASN][1000 genomes]
rs9865031	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1799287	chr3:150125721-150147118	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9826729	TSC22D2	cis	cerebellum	SCAN
rs9826729	UBQLN4	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150131000-150152000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:150131000-150166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:150132400-150146000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:150132400-150151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:150132400-150151600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:150132400-150159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:150132400-150160400	Weak transcription	Pancreas	Pancrea
8	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
10	chr3:150132600-150145200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:150132800-150145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:150132800-150145800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:150132800-150151000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:150133600-150151000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:150133600-150159200	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:150133600-150159200	Weak transcription	Left Ventricle	heart
17	chr3:150133800-150159200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:150134000-150143000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:150134000-150143800	Weak transcription	Aorta	Aorta
20	chr3:150134000-150146000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:150134000-150147000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:150134000-150159200	Weak transcription	Thymus	Thymus
23	chr3:150134600-150146000	Weak transcription	Stomach Mucosa	stomach
24	chr3:150134600-150174800	Weak transcription	Dnd41	blood
25	chr3:150135000-150175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:150135600-150145600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:150136000-150144000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:150136000-150145800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:150136000-150160800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:150136200-150142400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:150136200-150146000	Weak transcription	Psoas Muscle	Psoas
32	chr3:150136200-150160000	Weak transcription	Fetal Brain Male	brain
33	chr3:150136400-150142000	Enhancers	Fetal Lung	lung
34	chr3:150136400-150142400	Weak transcription	Fetal Thymus	thymus
35	chr3:150136400-150148000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:150136600-150144000	Weak transcription	Primary B cells from cord blood	blood
37	chr3:150137000-150141800	Enhancers	Brain Germinal Matrix	brain
38	chr3:150137200-150176200	Weak transcription	HepG2	liver
39	chr3:150137600-150148000	Weak transcription	Hela-S3	cervix
40	chr3:150137800-150142000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr3:150138000-150151200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:150138000-150151200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:150138000-150159400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:150138200-150143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:150138200-150144200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:150138200-150157400	Weak transcription	HSMMtube	muscle
47	chr3:150138200-150159400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:150138400-150146000	Weak transcription	Liver	Liver
49	chr3:150139000-150141800	Enhancers	Colon Smooth Muscle	Colon
50	chr3:150139200-150141800	Enhancers	Cortex derived primary cultured neurospheres	brain

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