Variant report

Variant	rs10513375
Chromosome Location	chr3:150147118-150147119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150146836..150150944-chr3:150211993..150216271,5	K562	blood:
2	chr3:150146603..150148392-chr3:150150774..150152594,2	MCF-7	breast:
3	chr3:150146418..150149679-chr3:150264097..150266286,3	K562	blood:
4	chr3:150146891..150148422-chr3:150153050..150155459,2	MCF-7	breast:
5	chr3:150138486..150140659-chr3:150145400..150147517,2	MCF-7	breast:
6	chr3:150145113..150147525-chr3:150161177..150163956,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144895	Chromatin interaction
ENSG00000120742	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10513368	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513370	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513371	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513372	1.00[CEU][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713072	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714034	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11714123	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925759	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11928577	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928948	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066114	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067910	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068946	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073230	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs13076419	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089766	0.87[EUR][1000 genomes]
rs13317818	0.89[ASN][1000 genomes]
rs1376027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278131	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28571974	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587291	0.89[ASN][1000 genomes]
rs2868430	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34106738	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156311	0.93[ASN][1000 genomes]
rs34419133	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503712	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34647320	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34983941	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35019980	0.87[EUR][1000 genomes]
rs35234277	0.82[ASN][1000 genomes]
rs35598887	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749400	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811719	0.89[ASN][1000 genomes]
rs61734437	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66816665	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67073112	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67100311	0.87[EUR][1000 genomes]
rs6791546	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799106	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799981	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73165716	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73167540	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7614772	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618493	0.89[ASN][1000 genomes]
rs7620193	0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7621019	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7623100	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827736	0.82[ASN][1000 genomes]
rs9844735	0.89[ASN][1000 genomes]
rs9875752	0.89[ASN][1000 genomes]
rs9879140	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv822291	chr3:150143146-150148557	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10513375	TSC22D2	cis	cerebellum	SCAN

Chromatin state (count:103 , 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	chr3:150132400-150151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:150132400-150151600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:150132400-150159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:150132400-150160400	Weak transcription	Pancreas	Pancrea
7	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
9	chr3:150132800-150151000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:150133600-150151000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:150133600-150159200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:150133600-150159200	Weak transcription	Left Ventricle	heart
13	chr3:150133800-150159200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:150134000-150159200	Weak transcription	Thymus	Thymus
15	chr3:150134600-150174800	Weak transcription	Dnd41	blood
16	chr3:150135000-150175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:150136000-150160800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:150136200-150160000	Weak transcription	Fetal Brain Male	brain
19	chr3:150136400-150148000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:150137200-150176200	Weak transcription	HepG2	liver
21	chr3:150137600-150148000	Weak transcription	Hela-S3	cervix
22	chr3:150138000-150151200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:150138000-150151200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:150138000-150159400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:150138200-150157400	Weak transcription	HSMMtube	muscle
26	chr3:150138200-150159400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:150139800-150148000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:150140000-150151400	Strong transcription	HSMM	muscle
29	chr3:150140000-150164000	Weak transcription	Fetal Intestine Small	intestine
30	chr3:150140000-150171800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:150140000-150176200	Weak transcription	Fetal Stomach	stomach
32	chr3:150140200-150147200	Weak transcription	Primary T cells from cord blood	blood
33	chr3:150140200-150151200	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:150140200-150160400	Weak transcription	Fetal Kidney	kidney
35	chr3:150141400-150175200	Weak transcription	GM12878-XiMat	blood
36	chr3:150141800-150159400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:150141800-150164400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:150141800-150165000	Weak transcription	Brain Germinal Matrix	brain
39	chr3:150141800-150166800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:150142000-150153800	Weak transcription	Fetal Lung	lung
41	chr3:150142000-150159400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:150143200-150159200	Weak transcription	Fetal Thymus	thymus
43	chr3:150143400-150152000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:150143800-150148400	Enhancers	Fetal Heart	heart
45	chr3:150143800-150149400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:150144000-150148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:150144000-150153400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:150144000-150159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:150144200-150179000	Weak transcription	Aorta	Aorta
50	chr3:150144400-150151000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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