Variant report

Variant	rs2654871
Chromosome Location	chr1:242612420-242612421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10158285	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926736	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10926738	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926742	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926743	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2008631	0.81[EUR][1000 genomes]
rs2249864	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2654868	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2654869	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2654870	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2810034	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2810035	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2810036	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2810037	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810038	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549463	chr1:242265419-242856854	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv430391	chr1:242307104-243280885	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv817488	chr1:242330066-243121127	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv868888	chr1:242330066-243191101	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1003844	chr1:242363698-242904755	Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv549464	chr1:242411114-242842300	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv549465	chr1:242465655-242989157	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1014487	chr1:242532959-243011891	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv535367	chr1:242532959-243011891	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv873377	chr1:242607583-243114662	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv945414	chr1:242610697-242858815	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242597800-242619000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:242599600-242612600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:242609800-242613200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:242609800-242613200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:242609800-242613400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:242609800-242613600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:242610000-242613400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:242610200-242613400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:242610800-242613000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:242611000-242613000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:242611000-242613600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:242611000-242632200	Weak transcription	HMEC	breast
13	chr1:242611200-242613200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:242611200-242615600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:242611400-242613200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:242611400-242613400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:242611400-242613600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:242611600-242612600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:242611800-242612800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:242611800-242612800	Active TSS	Brain Substantia Nigra	brain
21	chr1:242611800-242613200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:242611800-242613200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:242612000-242612800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:242612000-242612800	Active TSS	Brain Angular Gyrus	brain
25	chr1:242612000-242612800	Active TSS	Brain Hippocampus Middle	brain
26	chr1:242612000-242612800	Active TSS	Fetal Brain Female	brain
27	chr1:242612200-242612600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:242612200-242612600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:242612200-242612800	Enhancers	Fetal Kidney	kidney
30	chr1:242612200-242612800	Enhancers	Fetal Muscle Leg	muscle
31	chr1:242612200-242613200	Enhancers	Fetal Brain Male	brain
32	chr1:242612200-242613400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:242612200-242613600	Bivalent Enhancer	Fetal Lung	lung
34	chr1:242612400-242612800	Active TSS	Brain Cingulate Gyrus	brain
35	chr1:242612400-242613000	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr1:242612400-242613200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:242612400-242613200	Strong transcription	Aorta	Aorta
38	chr1:242612400-242613200	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr1:242612400-242613600	Enhancers	Fetal Stomach	stomach

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