Variant report

Variant	rs6935829
Chromosome Location	chr6:150217811-150217812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr6:150216385-150218199	HCT-116	colon:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217888-150217899 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
2	FOSL1	chr6:150216818-150218149	HCT-116	colon:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
3	CHD2	chr6:150217017-150217829	Hela-S3	cervix:	n/a	n/a
4	JUND	chr6:150217810-150217921	K562	blood:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217888-150217899 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
5	POLR2A	chr6:150216178-150217814	Hela-S3	cervix:	n/a	n/a
6	MYC	chr6:150217736-150217866	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr6:150217721-150218049	MCF10A-Er-Src	breast:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
8	TCF7L2	chr6:150216917-150217990	HCT-116	colon:	n/a	chr6:150217421-150217430 chr6:150217889-150217898
9	POLR2A	chr6:150217702-150218092	U87	brain:	n/a	n/a
10	TCF7L2	chr6:150216937-150217972	Hela-S3	cervix:	n/a	chr6:150217421-150217430 chr6:150217889-150217898
11	FOS	chr6:150217724-150218076	MCF10A-Er-Src	breast:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
12	FOS	chr6:150217152-150218119	HUVEC	blood vessel:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217336-150217347 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
13	SP1	chr6:150216244-150218167	HCT-116	colon:	n/a	chr6:150218010-150218017
14	JUND	chr6:150217047-150218020	Hela-S3	cervix:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217888-150217899 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
15	TCF12	chr6:150216862-150218267	SK-N-SH	brain:	n/a	n/a
16	FOS	chr6:150217742-150218032	MCF10A-Er-Src	breast:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
17	FOS	chr6:150217758-150218041	MCF10A-Er-Src	breast:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
18	SMARCC1	chr6:150217059-150218059	Hela-S3	cervix:	n/a	chr6:150217889-150217898

No.	Distal block	Cell Line	Cell type
1	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:
2	chr6:150183832..150186232-chr6:150215270..150224001,9	MCF-7	breast:
3	chr6:150212160..150213980-chr6:150214968..150218117,3	K562	blood:

Variant related genes	Relation type
RAET1E	TF binding region
ENSG00000203722	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000164520	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1334510	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17748069	0.89[ASN][1000 genomes]
rs2095376	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2342767	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2342768	0.87[EUR][1000 genomes]
rs2342769	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2342770	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823021	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4242281	0.80[ASN][1000 genomes]
rs4458704	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4869763	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869764	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4870109	0.80[ASN][1000 genomes]
rs4870116	0.91[EUR][1000 genomes]
rs6557133	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6933882	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6939761	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7740145	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7742692	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7742993	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7744821	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7747435	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7747457	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7753544	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7756850	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757972	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757984	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7758020	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7758033	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7763719	0.83[EUR][1000 genomes]
rs7763849	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7764376	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7767588	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7767592	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7768626	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7768665	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7769118	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7771014	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774787	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9322225	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322228	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9371215	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9371223	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9371504	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371505	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371533	0.96[EUR][1000 genomes]
rs9371541	0.88[AFR][1000 genomes]
rs9371542	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9371544	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9383584	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9383912	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9383913	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9383914	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9383921	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9383940	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9397058	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9397398	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9397420	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9397434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9478192	0.80[EUR][1000 genomes]
rs9478241	0.82[ASN][1000 genomes]
rs9968871	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9969044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9986576	0.80[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6935829	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs6935829	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs6935829	RAET1E	cis	Esophagus Mucosa	GTEx
rs6935829	RAET1G	cis	Thyroid	GTEx
rs6935829	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs6935829	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs6935829	LRP11	cis	Adipose Subcutaneous	GTEx
rs6935829	RP11-350J20.9	cis	lung	GTEx
rs6935829	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs6935829	RP11-350J20.5	cis	Thyroid	GTEx
rs6935829	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs6935829	RAET1E	cis	Nerve Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:150215800-150218200	Enhancers	Adipose Nuclei	Adipose
3	chr6:150215800-150219200	Enhancers	Stomach Mucosa	stomach
4	chr6:150216000-150218000	Enhancers	NHLF	lung
5	chr6:150216000-150218200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:150216000-150218200	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr6:150216000-150218200	Enhancers	Esophagus	oesophagus
8	chr6:150216000-150218200	Enhancers	Fetal Lung	lung
9	chr6:150216000-150218200	Enhancers	Ovary	ovary
10	chr6:150216000-150218200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr6:150216000-150218200	Enhancers	Spleen	Spleen
12	chr6:150216000-150218400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:150216000-150218400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:150216000-150218400	Enhancers	Colon Smooth Muscle	Colon
15	chr6:150216000-150218600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:150216000-150218600	Enhancers	Psoas Muscle	Psoas
17	chr6:150216000-150218800	Enhancers	Fetal Stomach	stomach
18	chr6:150216000-150219000	Enhancers	Placenta	Placenta
19	chr6:150216000-150219000	Enhancers	Right Atrium	heart
20	chr6:150216000-150219200	Enhancers	Left Ventricle	heart
21	chr6:150216000-150219400	Enhancers	Lung	lung
22	chr6:150216000-150219400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:150216000-150219400	Flanking Active TSS	Hela-S3	cervix
24	chr6:150216000-150222600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:150216200-150218000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:150216200-150218000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:150216200-150218000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:150216200-150218200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:150216200-150218400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:150216200-150218600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:150216200-150218800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:150216200-150219400	Enhancers	Fetal Intestine Large	intestine
33	chr6:150216200-150219400	Enhancers	Fetal Muscle Trunk	muscle
34	chr6:150216200-150219600	Enhancers	Fetal Muscle Leg	muscle
35	chr6:150216400-150218000	Enhancers	Liver	Liver
36	chr6:150216400-150218000	Enhancers	HSMMtube	muscle
37	chr6:150216400-150218800	Enhancers	HUVEC	blood vessel
38	chr6:150216400-150219000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr6:150216600-150218000	Enhancers	HSMM	muscle
40	chr6:150216600-150218200	Enhancers	Colonic Mucosa	Colon
41	chr6:150216600-150218200	Enhancers	NH-A	brain
42	chr6:150216600-150218400	Enhancers	Small Intestine	intestine
43	chr6:150216600-150219000	Flanking Active TSS	NHEK	skin
44	chr6:150216600-150219200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:150216600-150221800	Weak transcription	Pancreas	Pancrea
46	chr6:150216600-150225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:150216800-150218000	Enhancers	Aorta	Aorta
48	chr6:150216800-150218600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:150216800-150218600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:150216800-150219000	Enhancers	Brain Cingulate Gyrus	brain

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