Variant report

Variant	rs9376753
Chromosome Location	chr6:143816123-143816124
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143815651..143818272-chr6:143830902..143832813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001036	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1061220	0.87[JPT][hapmap]
rs1065355	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs10782288	0.88[EUR][1000 genomes]
rs10782289	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10809	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12196227	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12199192	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1338533	0.90[EUR][1000 genomes]
rs1424922	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1569589	0.90[ASW][hapmap]
rs1978529	0.93[EUR][1000 genomes]
rs2143137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272924	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs2294505	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2294506	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs2496593	0.82[JPT][hapmap]
rs3088203	0.87[JPT][hapmap]
rs3761999	0.81[JPT][hapmap]
rs3762000	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs3762001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789789	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804538	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804539	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804544	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895612	0.81[JPT][hapmap]
rs4895614	0.81[JPT][hapmap]
rs4895615	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs4896656	0.81[JPT][hapmap]
rs4896659	0.87[EUR][1000 genomes]
rs4896660	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs6924268	0.88[EUR][1000 genomes]
rs6926733	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs6929191	0.81[JPT][hapmap]
rs6930325	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6935346	0.94[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6935618	0.94[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs7741976	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751011	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9321913	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9321914	0.94[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs9373391	0.81[JPT][hapmap]
rs9373393	0.94[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs9376750	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9390092	0.81[JPT][hapmap]
rs9390094	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9390096	1.00[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.88[EUR][1000 genomes]
rs9399442	0.86[EUR][1000 genomes]
rs9399443	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403492	0.87[EUR][1000 genomes]
rs9403494	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403496	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv965776	chr6:143811602-143816945	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9376753	HIVEP2	cis	parietal	SCAN
rs9376753	FUCA2	cis	parietal	SCAN
rs9376753	RAB32	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143772600-143832000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:143772800-143821200	Weak transcription	Psoas Muscle	Psoas
3	chr6:143773200-143827000	Weak transcription	Brain Germinal Matrix	brain
4	chr6:143773400-143818200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:143773400-143832000	Weak transcription	Fetal Brain Male	brain
6	chr6:143774400-143819400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:143779000-143818200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:143779200-143816800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:143781000-143832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:143783200-143818400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:143790200-143831600	Weak transcription	Esophagus	oesophagus
12	chr6:143790200-143831600	Weak transcription	Gastric	stomach
13	chr6:143793600-143819400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:143794600-143819400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:143794800-143817800	Weak transcription	HSMMtube	muscle
16	chr6:143795200-143827400	Weak transcription	Aorta	Aorta
17	chr6:143795800-143831800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:143797000-143826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:143797400-143819200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:143797600-143831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:143798000-143817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:143798200-143819400	Weak transcription	Fetal Thymus	thymus
23	chr6:143798400-143819400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:143798800-143819600	Weak transcription	Fetal Brain Female	brain
25	chr6:143798800-143821400	Weak transcription	HMEC	breast
26	chr6:143799000-143827000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:143799400-143816600	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:143799400-143819200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:143800600-143818000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:143800800-143831000	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:143801200-143819400	Weak transcription	Dnd41	blood
32	chr6:143802200-143818600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:143805200-143827800	Weak transcription	Fetal Heart	heart
34	chr6:143808000-143818200	Weak transcription	Brain Angular Gyrus	brain
35	chr6:143808600-143818400	Weak transcription	Primary B cells from cord blood	blood
36	chr6:143809800-143817600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:143811400-143832000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:143811800-143829400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:143812000-143827400	Weak transcription	Pancreas	Pancrea
40	chr6:143812200-143819400	Weak transcription	Thymus	Thymus
41	chr6:143812200-143831600	Weak transcription	Right Ventricle	heart
42	chr6:143812400-143816600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:143812400-143818200	Weak transcription	Fetal Stomach	stomach
44	chr6:143812400-143820800	Weak transcription	Lung	lung
45	chr6:143812400-143826800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:143812400-143829600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:143812400-143832200	Weak transcription	Spleen	Spleen
48	chr6:143812600-143831800	Weak transcription	NHEK	skin
49	chr6:143812600-143832000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:143812800-143818800	Weak transcription	Primary T cells from cord blood	blood

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