Variant report

Variant	rs6683078
Chromosome Location	chr1:154473726-154473727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154473384..154476326-chr1:154529885..154532539,2	MCF-7	breast:
2	chr1:154191216..154193063-chr1:154472171..154474701,2	K562	blood:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10752642	0.81[YRI][hapmap]
rs1113142	1.00[EUR][1000 genomes]
rs11265605	1.00[EUR][1000 genomes]
rs11265627	0.81[YRI][hapmap]
rs11265630	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194591	1.00[EUR][1000 genomes]
rs1194594	1.00[EUR][1000 genomes]
rs1205590	1.00[EUR][1000 genomes]
rs1685625	1.00[EUR][1000 genomes]
rs1685626	1.00[EUR][1000 genomes]
rs1817688	1.00[EUR][1000 genomes]
rs2340487	1.00[EUR][1000 genomes]
rs4072391	0.88[YRI][hapmap]
rs4078519	1.00[EUR][1000 genomes]
rs4240873	0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4393148	0.94[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4474240	0.83[ASW][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs4518898	0.81[YRI][hapmap]
rs4520411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845369	1.00[EUR][1000 genomes]
rs4845632	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845635	0.82[YRI][hapmap]
rs4845646	0.89[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55649582	1.00[EUR][1000 genomes]
rs55857358	1.00[EUR][1000 genomes]
rs6427694	0.89[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6427716	0.81[YRI][hapmap]
rs6666943	1.00[EUR][1000 genomes]
rs6670375	0.81[YRI][hapmap]
rs6678164	0.94[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681961	0.97[AFR][1000 genomes]
rs6684225	0.94[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6687112	0.81[YRI][hapmap]
rs6691727	0.81[YRI][hapmap]
rs7513603	0.81[YRI][hapmap]
rs7515974	0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527520	1.00[EUR][1000 genomes]
rs7529744	1.00[MEX][hapmap]
rs7530737	0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537595	1.00[EUR][1000 genomes]
rs7539745	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs7556118	1.00[EUR][1000 genomes]
rs9659545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9728545	0.94[AFR][1000 genomes]
rs9804125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	esv1815481	chr1:154465065-154475033	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv3424713	chr1:154473153-154475701	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	esv3414034	chr1:154473478-154476776	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154461800-154473800	Weak transcription	Pancreas	Pancrea
2	chr1:154471200-154474000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
3	chr1:154471200-154475400	Active TSS	Right Atrium	heart
4	chr1:154471600-154473800	Active TSS	Right Ventricle	heart
5	chr1:154471800-154473800	Bivalent/Poised TSS	Fetal Stomach	stomach
6	chr1:154471800-154473800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
7	chr1:154471800-154474200	Bivalent/Poised TSS	Psoas Muscle	Psoas
8	chr1:154472000-154475200	Bivalent/Poised TSS	Left Ventricle	heart
9	chr1:154472200-154473800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
10	chr1:154472200-154473800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
11	chr1:154472200-154475400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:154472200-154475400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
13	chr1:154472400-154473800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
14	chr1:154472400-154474000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
15	chr1:154472400-154474000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
16	chr1:154472400-154474400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
17	chr1:154472400-154475400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
18	chr1:154472600-154473800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr1:154472600-154474000	Bivalent/Poised TSS	Fetal Kidney	kidney
20	chr1:154472600-154474200	Bivalent/Poised TSS	Fetal Lung	lung
21	chr1:154472800-154473800	Bivalent/Poised TSS	Colonic Mucosa	Colon
22	chr1:154472800-154473800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr1:154472800-154473800	Bivalent/Poised TSS	Placenta	Placenta
24	chr1:154472800-154473800	Active TSS	Ovary	ovary
25	chr1:154472800-154474800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:154472800-154475200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:154472800-154475200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
28	chr1:154472800-154475200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr1:154473000-154473800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
30	chr1:154473000-154474000	Active TSS	Spleen	Spleen
31	chr1:154473000-154474200	Bivalent/Poised TSS	Fetal Thymus	thymus
32	chr1:154473000-154475000	Active TSS	Lung	lung
33	chr1:154473200-154474400	Flanking Active TSS	Liver	Liver
34	chr1:154473200-154475200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr1:154473200-154475200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
36	chr1:154473200-154475600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
37	chr1:154473200-154475600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:154473400-154473800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
39	chr1:154473400-154474800	Bivalent/Poised TSS	Aorta	Aorta
40	chr1:154473400-154475000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr1:154473400-154475200	Active TSS	HUVEC	blood vessel
42	chr1:154473400-154475400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
43	chr1:154473600-154473800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr1:154473600-154473800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
45	chr1:154473600-154474000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:154473600-154474000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr1:154473600-154474200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links