Variant report

Variant	rs6666943
Chromosome Location	chr1:154247254-154247255
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154191842..154194909-chr1:154241050..154247826,7	K562	blood:
2	chr1:154244884..154247394-chr1:154296390..154298976,2	K562	blood:
3	chr1:154246983..154251176-chr1:154298435..154300962,3	MCF-7	breast:
4	chr1:153962343..153963954-chr1:154245938..154247539,2	K562	blood:
5	chr1:154236442..154241812-chr1:154243586..154247600,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177954	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1113142	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11265238	0.88[YRI][hapmap]
rs11265605	1.00[EUR][1000 genomes]
rs1194581	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1194591	1.00[EUR][1000 genomes]
rs1194594	0.84[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194597	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs1194601	1.00[EUR][1000 genomes]
rs1194605	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs12026177	0.84[YRI][hapmap]
rs12028949	0.84[YRI][hapmap]
rs1205590	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs16835846	0.84[YRI][hapmap]
rs16835909	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1685625	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1685626	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1760801	0.81[AFR][1000 genomes]
rs1817688	1.00[EUR][1000 genomes]
rs2340487	1.00[EUR][1000 genomes]
rs2500222	1.00[EUR][1000 genomes]
rs2633434	0.86[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3811455	0.84[YRI][hapmap]
rs3935419	0.84[YRI][hapmap]
rs4393148	1.00[EUR][1000 genomes]
rs4406621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845369	1.00[EUR][1000 genomes]
rs4845632	1.00[EUR][1000 genomes]
rs55649582	1.00[EUR][1000 genomes]
rs55650526	1.00[EUR][1000 genomes]
rs55664806	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55857358	1.00[EUR][1000 genomes]
rs56752149	1.00[EUR][1000 genomes]
rs56760430	1.00[EUR][1000 genomes]
rs59310765	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59651124	1.00[EUR][1000 genomes]
rs60506384	1.00[EUR][1000 genomes]
rs60743909	1.00[EUR][1000 genomes]
rs6427694	1.00[EUR][1000 genomes]
rs6683078	1.00[EUR][1000 genomes]
rs715737	0.89[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7515974	1.00[EUR][1000 genomes]
rs7527520	1.00[EUR][1000 genomes]
rs7556118	1.00[EUR][1000 genomes]
rs9804125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154245800-154247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154245800-154248400	Weak transcription	Aorta	Aorta
3	chr1:154246000-154247400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:154246000-154247400	Weak transcription	Small Intestine	intestine
5	chr1:154246000-154247600	Weak transcription	Esophagus	oesophagus
6	chr1:154246000-154249200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:154246200-154247400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:154246200-154247400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:154246200-154247400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:154246200-154247400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:154246200-154247600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:154246200-154247600	Weak transcription	Gastric	stomach
13	chr1:154246200-154247600	Weak transcription	Pancreas	Pancrea
14	chr1:154246200-154247600	Weak transcription	Right Ventricle	heart
15	chr1:154246200-154247600	Weak transcription	A549	lung
16	chr1:154246200-154248200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:154246200-154249400	Weak transcription	HMEC	breast
18	chr1:154246200-154249600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:154246200-154249600	Weak transcription	HSMMtube	muscle
20	chr1:154246200-154249600	Weak transcription	NHLF	lung
21	chr1:154246200-154250800	Weak transcription	Fetal Brain Male	brain
22	chr1:154246200-154259400	Weak transcription	Right Atrium	heart
23	chr1:154246400-154247400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:154246400-154247400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:154246400-154247400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:154246400-154247400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:154246400-154247400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:154246400-154247400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:154246400-154247400	Weak transcription	Left Ventricle	heart
30	chr1:154246400-154247400	Weak transcription	Lung	lung
31	chr1:154246400-154247400	Weak transcription	Psoas Muscle	Psoas
32	chr1:154246400-154247400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:154246400-154247400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:154246400-154247400	Weak transcription	GM12878-XiMat	blood
35	chr1:154246400-154247600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:154246400-154247600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:154246400-154248000	Weak transcription	Brain Angular Gyrus	brain
38	chr1:154246400-154248200	Strong transcription	Brain Anterior Caudate	brain
39	chr1:154246400-154248400	Strong transcription	Colon Smooth Muscle	Colon
40	chr1:154246400-154248400	Genic enhancers	K562	blood
41	chr1:154246400-154249000	Weak transcription	Fetal Heart	heart
42	chr1:154246400-154249400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:154246400-154249400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:154246400-154249400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:154246400-154249600	Weak transcription	Brain Substantia Nigra	brain
46	chr1:154246400-154249600	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:154246400-154249800	Weak transcription	HSMM	muscle
48	chr1:154246400-154249800	Weak transcription	HUVEC	blood vessel
49	chr1:154246400-154250800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:154246400-154250800	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links