Variant report

Variant	rs7329615
Chromosome Location	chr13:48582318-48582319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48582295..48583962-chr13:48609861..48612034,3	MCF-7	breast:
2	chr13:48582197..48584470-chr13:48587101..48588895,3	K562	blood:
3	chr13:48574374..48577115-chr13:48582197..48584220,3	MCF-7	breast:
4	chr13:48582197..48584034-chr13:48587167..48588895,2	K562	blood:

Variant related genes	Relation type
ENSG00000136159	Chromatin interaction
ENSG00000227848	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1104351	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12427516	1.00[JPT][hapmap]
rs12429348	1.00[JPT][hapmap]
rs12869161	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968029	1.00[JPT][hapmap]
rs1998988	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2025864	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2104481	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148939	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2148940	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182374	1.00[JPT][hapmap]
rs2182378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406694	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3990876	0.80[AMR][1000 genomes]
rs4427704	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4941618	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7317685	0.87[AMR][1000 genomes]
rs7323702	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7335797	1.00[JPT][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]
rs7336170	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753372	1.00[JPT][hapmap]
rs7985469	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001032	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	1.00[JPT][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]
rs8002847	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs840428	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	1.00[JPT][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]
rs840435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526448	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526454	0.87[AMR][1000 genomes]
rs9526455	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9534884	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534934	1.00[JPT][hapmap]
rs9534956	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9534966	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9562792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567927	1.00[JPT][hapmap]
rs9567988	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7329615	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs7329615	MED4	cis	multi-tissue	Pritchard
rs7329615	SUCLA2	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48576000-48582800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:48576000-48583200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr13:48576000-48583600	Weak transcription	HSMMtube	muscle
6	chr13:48576000-48583800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:48576000-48587000	Weak transcription	Primary B cells from cord blood	blood
8	chr13:48576000-48587000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr13:48576000-48588400	Weak transcription	Fetal Intestine Large	intestine
10	chr13:48576000-48589800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr13:48576000-48590800	Weak transcription	Gastric	stomach
12	chr13:48576000-48603600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr13:48576000-48604000	Weak transcription	Primary T cells from cord blood	blood
14	chr13:48576000-48604800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr13:48576000-48604800	Weak transcription	Fetal Stomach	stomach
16	chr13:48576000-48604800	Weak transcription	Thymus	Thymus
17	chr13:48576000-48610800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr13:48576000-48611400	Weak transcription	Left Ventricle	heart
19	chr13:48576200-48592000	Weak transcription	Fetal Intestine Small	intestine
20	chr13:48576400-48589000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr13:48576400-48605000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr13:48576600-48583200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr13:48576600-48583600	Weak transcription	Placenta	Placenta
24	chr13:48576600-48604800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:48576600-48604800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr13:48576600-48604800	Weak transcription	Dnd41	blood
27	chr13:48576600-48610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:48578800-48582400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr13:48578800-48583200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr13:48578800-48583600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr13:48578800-48583800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:48579600-48583600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:48579800-48583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr13:48579800-48583600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr13:48580800-48583000	Weak transcription	HSMM	muscle
36	chr13:48581000-48582400	Weak transcription	Hela-S3	cervix
37	chr13:48581200-48582400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:48581200-48582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:48581400-48582400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:48581400-48582400	Weak transcription	HMEC	breast
41	chr13:48582000-48584400	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links