Variant report

Variant	rs73924816
Chromosome Location	chr2:39481107-39481108
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39476355..39478295-chr2:39480403..39482715,2	MCF-7	breast:
2	chr2:39476438..39480963-chr2:39481034..39484561,4	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10199948	0.89[EUR][1000 genomes]
rs10490305	0.83[ASN][1000 genomes]
rs11886110	0.91[ASN][1000 genomes]
rs11888511	1.00[EUR][1000 genomes]
rs11898025	1.00[EUR][1000 genomes]
rs11898704	0.83[ASN][1000 genomes]
rs11902188	0.83[ASN][1000 genomes]
rs17023405	1.00[EUR][1000 genomes]
rs17023552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17023573	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17023584	1.00[EUR][1000 genomes]
rs17038958	0.83[ASN][1000 genomes]
rs2708227	0.95[EUR][1000 genomes]
rs3770661	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797011	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55961227	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56024079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56361338	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56850142	0.91[ASN][1000 genomes]
rs56928728	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57271382	1.00[EUR][1000 genomes]
rs57401773	1.00[EUR][1000 genomes]
rs58005382	0.91[ASN][1000 genomes]
rs58824151	0.91[ASN][1000 genomes]
rs59121834	1.00[EUR][1000 genomes]
rs59459399	0.83[ASN][1000 genomes]
rs59707152	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61219633	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61257289	1.00[EUR][1000 genomes]
rs6544201	0.83[EUR][1000 genomes]
rs6544206	1.00[EUR][1000 genomes]
rs6544207	0.89[EUR][1000 genomes]
rs6706379	0.83[EUR][1000 genomes]
rs6710707	0.83[EUR][1000 genomes]
rs6712399	0.83[ASN][1000 genomes]
rs6715143	0.83[EUR][1000 genomes]
rs6718000	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6725784	0.83[ASN][1000 genomes]
rs6727395	0.83[ASN][1000 genomes]
rs6731330	1.00[EUR][1000 genomes]
rs6746820	0.83[EUR][1000 genomes]
rs6755534	0.89[EUR][1000 genomes]
rs6759248	0.83[EUR][1000 genomes]
rs72921023	1.00[EUR][1000 genomes]
rs72925446	0.83[EUR][1000 genomes]
rs72927494	1.00[EUR][1000 genomes]
rs73923836	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73923844	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73923847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73923887	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73923888	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923889	0.91[ASN][1000 genomes]
rs73923895	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924810	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924817	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73930526	1.00[EUR][1000 genomes]
rs73930538	1.00[EUR][1000 genomes]
rs7569943	1.00[EUR][1000 genomes]
rs7584699	0.83[EUR][1000 genomes]
rs7588265	0.89[EUR][1000 genomes]
rs7588424	0.83[EUR][1000 genomes]
rs7589576	0.83[EUR][1000 genomes]
rs7591563	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7595047	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595102	1.00[EUR][1000 genomes]
rs7596222	0.89[EUR][1000 genomes]
rs7599017	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	35 gene(s)	inside rSNPs	diseases
12	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv2693	chr2:39468641-39513800	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39469200-39503800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:39469400-39504200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39471000-39503400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:39471200-39483800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39471200-39503800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:39471200-39504200	Weak transcription	Esophagus	oesophagus
7	chr2:39471400-39503400	Weak transcription	Right Ventricle	heart
8	chr2:39472600-39504000	Weak transcription	Thymus	Thymus
9	chr2:39472800-39492000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:39473000-39482600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:39473000-39485600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:39473000-39491000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:39473000-39492200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:39473200-39491400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:39474600-39482400	Strong transcription	HSMM	muscle
17	chr2:39474600-39492600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:39474600-39494600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:39474600-39494600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:39474800-39492600	Weak transcription	Psoas Muscle	Psoas
21	chr2:39475000-39483000	Strong transcription	NH-A	brain
22	chr2:39475600-39493600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:39475600-39494200	Strong transcription	Placenta	Placenta
24	chr2:39475600-39494400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:39475800-39481800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:39475800-39481800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:39475800-39482200	Strong transcription	Adipose Nuclei	Adipose
28	chr2:39476200-39483800	Weak transcription	Hela-S3	cervix
29	chr2:39476200-39502400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:39476400-39484600	Strong transcription	HepG2	liver
31	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:39476800-39483800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:39477000-39487800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:39477200-39481800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:39477200-39495200	Strong transcription	Liver	Liver
36	chr2:39477400-39481800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:39477400-39482200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr2:39477400-39482800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:39477600-39481600	Strong transcription	Primary T cells from cord blood	blood
40	chr2:39477600-39481800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:39477600-39481800	Strong transcription	Brain Anterior Caudate	brain
42	chr2:39477600-39481800	Strong transcription	Fetal Thymus	thymus
43	chr2:39477600-39481800	Strong transcription	Ovary	ovary
44	chr2:39477600-39481800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:39477600-39482000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:39477600-39483000	Strong transcription	HSMMtube	muscle
47	chr2:39477600-39484400	Strong transcription	Fetal Kidney	kidney
48	chr2:39477600-39487800	Strong transcription	Fetal Muscle Leg	muscle
49	chr2:39477600-39487800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr2:39477600-39488400	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links