Variant report

Variant	rs10513374
Chromosome Location	chr3:150148031-150148032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150138598..150140801-chr3:150147562..150149502,2	MCF-7	breast:
2	chr3:150146836..150150944-chr3:150211993..150216271,5	K562	blood:
3	chr3:150146603..150148392-chr3:150150774..150152594,2	MCF-7	breast:
4	chr3:150146418..150149679-chr3:150264097..150266286,3	K562	blood:
5	chr3:149628108..149630690-chr3:150147298..150149080,2	K562	blood:
6	chr3:150146891..150148422-chr3:150153050..150155459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120742	Chromatin interaction
ENSG00000082996	Chromatin interaction
ENSG00000144895	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10513373	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs10935800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711035	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719977	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12638309	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639090	0.85[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[ASN][1000 genomes]
rs13069723	0.91[AFR][1000 genomes]
rs13081231	0.99[ASN][1000 genomes]
rs13082720	0.80[ASN][1000 genomes]
rs13099758	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13321876	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs16862644	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs16862648	0.81[LWK][hapmap]
rs16862676	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1868672	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs1868673	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs28514580	0.80[ASN][1000 genomes]
rs28517277	0.90[AFR][1000 genomes]
rs2868425	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4423794	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.88[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];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4681206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58628422	0.99[ASN][1000 genomes]
rs62269065	0.87[AFR][1000 genomes]
rs67319423	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762432	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6770424	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs6784048	0.99[ASN][1000 genomes]
rs6792734	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792759	0.81[JPT][hapmap]
rs6795124	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6810143	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs73165707	0.84[ASN][1000 genomes]
rs7427177	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7626725	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651353	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651989	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs879634	0.85[AFR][1000 genomes]
rs9289809	0.84[CEU][hapmap]
rs9289810	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs9784335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813752	0.80[ASN][1000 genomes]
rs9826729	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]
rs9846873	0.81[ASN][1000 genomes]
rs9865031	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[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	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
rs10513374	GPR171	cis	parietal	SCAN

Chromatin state (count:102 , 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	chr3:150137200-150176200	Weak transcription	HepG2	liver
20	chr3:150138000-150151200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:150138000-150151200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:150138000-150159400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:150138200-150157400	Weak transcription	HSMMtube	muscle
24	chr3:150138200-150159400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:150140000-150151400	Strong transcription	HSMM	muscle
26	chr3:150140000-150164000	Weak transcription	Fetal Intestine Small	intestine
27	chr3:150140000-150171800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:150140000-150176200	Weak transcription	Fetal Stomach	stomach
29	chr3:150140200-150151200	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:150140200-150160400	Weak transcription	Fetal Kidney	kidney
31	chr3:150141400-150175200	Weak transcription	GM12878-XiMat	blood
32	chr3:150141800-150159400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:150141800-150164400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:150141800-150165000	Weak transcription	Brain Germinal Matrix	brain
35	chr3:150141800-150166800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:150142000-150153800	Weak transcription	Fetal Lung	lung
37	chr3:150142000-150159400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:150143200-150159200	Weak transcription	Fetal Thymus	thymus
39	chr3:150143400-150152000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:150143800-150148400	Enhancers	Fetal Heart	heart
41	chr3:150143800-150149400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:150144000-150148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:150144000-150153400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:150144000-150159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:150144200-150179000	Weak transcription	Aorta	Aorta
46	chr3:150144400-150151000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:150144400-150151200	Weak transcription	Right Atrium	heart
48	chr3:150144800-150148400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:150145000-150148200	Weak transcription	Primary B cells from cord blood	blood
50	chr3:150145000-150151600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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