Variant report

Variant	rs6848029
Chromosome Location	chr4:78812913-78812914
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78811376..78813925-chr4:78816983..78819701,2	K562	blood:
2	chr4:78740102..78741887-chr4:78811367..78813986,2	K562	blood:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10033527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10033613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097938	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11729215	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12645742	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13101418	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13101987	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13103035	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13103523	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13104947	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13106067	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13119606	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13120272	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16996915	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17002849	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088992	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2134050	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28404443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28855210	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34830788	0.84[ASN][1000 genomes]
rs35648590	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35735677	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35979107	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4453957	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4571357	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577601	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859511	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859877	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4859879	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4859888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859889	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62302728	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62302732	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533282	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533291	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533344	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533345	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66825464	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6811736	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6814912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6854895	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7670157	0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7675009	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7676660	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7698627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs905376	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6848029	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs6848029	MRPL1	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
2	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
3	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
7	chr4:78785200-78816200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:78785200-78818800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:78785200-78820800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
11	chr4:78790600-78843400	Weak transcription	Small Intestine	intestine
12	chr4:78790800-78817400	Weak transcription	NH-A	brain
13	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
14	chr4:78794200-78815600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:78794200-78851800	Weak transcription	Lung	lung
16	chr4:78795600-78814600	Weak transcription	HSMM	muscle
17	chr4:78795600-78831800	Weak transcription	NHLF	lung
18	chr4:78795600-78833000	Weak transcription	Brain Germinal Matrix	brain
19	chr4:78799200-78832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:78802400-78814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
22	chr4:78803400-78814600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:78803400-78817600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr4:78806000-78813600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:78806000-78817600	Weak transcription	HMEC	breast
26	chr4:78806000-78817800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:78806000-78841400	Weak transcription	A549	lung
28	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
30	chr4:78807200-78813600	Weak transcription	NHDF-Ad	bronchial
31	chr4:78807400-78818200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr4:78808800-78814400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:78808800-78819000	Weak transcription	NHEK	skin
34	chr4:78808800-78820600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:78809000-78813800	Weak transcription	Pancreas	Pancrea
37	chr4:78809000-78817400	Weak transcription	K562	blood
38	chr4:78809000-78818400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:78809000-78825000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr4:78809200-78815800	Weak transcription	HUVEC	blood vessel
41	chr4:78809200-78836800	Weak transcription	Fetal Brain Female	brain
42	chr4:78809200-78837400	Weak transcription	Fetal Brain Male	brain
43	chr4:78809200-78847000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:78809400-78813400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:78809400-78813800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:78809400-78813800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:78809400-78814200	Weak transcription	Placenta	Placenta
48	chr4:78809400-78814200	Weak transcription	GM12878-XiMat	blood
49	chr4:78809400-78815400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:78809400-78815800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links