Variant report

Variant	rs55890805
Chromosome Location	chr2:39321988-39321989
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39318488..39322195-chr2:39323167..39328240,4	K562	blood:
2	chr2:39317005..39318517-chr2:39320324..39322079,2	K562	blood:
3	chr2:39319265..39325749-chr2:39345590..39349573,11	MCF-7	breast:
4	chr2:39321313..39323497-chr2:39324188..39326712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225900	Chromatin interaction
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10184046	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10184855	1.00[EUR][1000 genomes]
rs10186842	1.00[EUR][1000 genomes]
rs10188701	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10189440	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10196863	1.00[EUR][1000 genomes]
rs10199955	1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10203565	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10207187	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207984	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13394446	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13411756	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13416725	1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs13425165	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13428418	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13432395	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1451278	1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[EUR][1000 genomes]
rs17023214	1.00[EUR][1000 genomes]
rs17023241	1.00[EUR][1000 genomes]
rs17023292	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1901290	1.00[EUR][1000 genomes]
rs3099953	1.00[EUR][1000 genomes]
rs3112177	1.00[EUR][1000 genomes]
rs56269328	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56724744	1.00[EUR][1000 genomes]
rs57359008	1.00[EUR][1000 genomes]
rs59259697	1.00[EUR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61596046	1.00[EUR][1000 genomes]
rs6544200	1.00[EUR][1000 genomes]
rs6734212	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6737680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs72925431	1.00[EUR][1000 genomes]
rs72925433	1.00[EUR][1000 genomes]
rs72925439	1.00[EUR][1000 genomes]
rs7340303	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930506	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7564481	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7565814	1.00[EUR][1000 genomes]
rs7571608	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7571719	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7574214	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7589303	1.00[EUR][1000 genomes]
rs7599990	1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
2	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
3	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
4	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:39282600-39327400	Weak transcription	Hela-S3	cervix
7	chr2:39293600-39322000	Weak transcription	NHDF-Ad	bronchial
8	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
10	chr2:39294200-39322000	Weak transcription	Dnd41	blood
11	chr2:39294400-39322000	Weak transcription	HSMM	muscle
12	chr2:39294600-39339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:39294800-39322000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:39296400-39322600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:39296400-39339400	Weak transcription	Aorta	Aorta
16	chr2:39296600-39322200	Weak transcription	NHEK	skin
17	chr2:39297200-39322000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:39297400-39324600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:39301200-39322200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:39305800-39322000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:39307600-39324600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:39307600-39333800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:39311000-39322000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:39311200-39322000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:39311600-39322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:39313600-39322000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:39314000-39322000	Weak transcription	Ovary	ovary
28	chr2:39315200-39326800	Weak transcription	Psoas Muscle	Psoas
29	chr2:39316600-39322000	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:39316600-39324800	Weak transcription	Placenta	Placenta
31	chr2:39318400-39322000	Weak transcription	Fetal Intestine Small	intestine
32	chr2:39318400-39322200	Weak transcription	Primary T cells from cord blood	blood
33	chr2:39318600-39322000	Weak transcription	Fetal Stomach	stomach
34	chr2:39319000-39322000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:39319000-39333800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:39319200-39322000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:39319400-39322000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:39319600-39322000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:39319600-39322000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:39319600-39327800	Weak transcription	Lung	lung
41	chr2:39319600-39328200	Weak transcription	Right Atrium	heart
42	chr2:39319600-39339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:39319800-39333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:39320600-39323200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:39320600-39323200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr2:39320600-39323400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr2:39320600-39323600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr2:39320800-39322000	Weak transcription	Fetal Lung	lung
50	chr2:39320800-39322800	Enhancers	Fetal Thymus	thymus

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