Variant report

Variant	rs6684076
Chromosome Location	chr1:217200953-217200954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:217200941..217201873-chr6:54053550..54054293,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11572427	0.86[CEU][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11572435	0.86[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11577589	0.81[CEU][hapmap];0.83[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11585218	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11585774	0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12723476	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12724974	0.86[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12731437	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.82[EUR][1000 genomes]
rs12738035	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs12741457	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12747869	0.81[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12750129	0.81[CEU][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12756498	0.85[CEU][hapmap];0.83[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12759546	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12759584	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17044977	1.00[ASW][hapmap];0.86[CEU][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17635718	0.93[CEU][hapmap]
rs17636663	0.80[CEU][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17686743	0.86[CEU][hapmap]
rs17686866	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap]
rs1890555	0.85[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34493634	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34904258	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35185630	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35409092	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35701761	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4846800	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap]
rs6681177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71643439	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs867409	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6684076	NSL1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217194800-217206200	Weak transcription	Left Ventricle	heart
2	chr1:217196000-217206200	Weak transcription	Right Atrium	heart
3	chr1:217196200-217206200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:217198600-217203200	Weak transcription	Aorta	Aorta
5	chr1:217199200-217204800	Enhancers	Fetal Kidney	kidney
6	chr1:217199600-217202400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:217199600-217203800	Enhancers	Fetal Intestine Large	intestine
8	chr1:217199600-217206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:217199600-217211800	Weak transcription	Gastric	stomach
10	chr1:217199800-217202800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:217199800-217203400	Enhancers	Fetal Intestine Small	intestine
12	chr1:217200000-217201400	Enhancers	Primary B cells from cord blood	blood
13	chr1:217200000-217201800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:217200000-217202000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:217200000-217203600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:217200200-217201000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:217200200-217203200	Weak transcription	Pancreas	Pancrea
18	chr1:217200400-217201200	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:217200400-217201400	Enhancers	GM12878-XiMat	blood
20	chr1:217200400-217202400	Weak transcription	Stomach Mucosa	stomach
21	chr1:217200400-217202600	Weak transcription	Psoas Muscle	Psoas
22	chr1:217200400-217203000	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:217200600-217201800	Enhancers	Brain Anterior Caudate	brain
24	chr1:217200600-217204000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:217200800-217201000	Enhancers	Fetal Heart	heart
26	chr1:217200800-217201800	Enhancers	Brain Substantia Nigra	brain
27	chr1:217200800-217202200	Weak transcription	Small Intestine	intestine

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