Variant report

Variant	rs2919126
Chromosome Location	chr2:55207895-55207896
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	chr2:55204435..55209089-chr2:55274911..55278052,4	MCF-7	breast:
2	chr2:55205322..55208790-chr2:55211251..55214642,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1012603	0.83[AFR][1000 genomes]
rs13031431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17046514	0.83[AFR][1000 genomes]
rs17046579	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17046586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17046589	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17046643	0.83[AFR][1000 genomes]
rs1822617	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2241958	0.83[AFR][1000 genomes]
rs2255026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255393	0.83[CHB][hapmap]
rs2580768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2580769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2580770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2580771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2588513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2588515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588522	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972063	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34352825	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34378852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34928331	0.92[ASN][1000 genomes]
rs35981204	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4672003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672006	0.83[AFR][1000 genomes]
rs4672009	0.83[AFR][1000 genomes]
rs57737203	0.83[AFR][1000 genomes]
rs60553807	0.83[AFR][1000 genomes]
rs6545464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739210	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72795434	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7355716	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55193400-55214800	Strong transcription	HepG2	liver
5	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:55195000-55215200	Strong transcription	Dnd41	blood
9	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
13	chr2:55196600-55208400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55198600-55215200	Weak transcription	Lung	lung
19	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:55199400-55208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:55200200-55209600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
24	chr2:55200800-55208000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
26	chr2:55201000-55208400	Weak transcription	Placenta	Placenta
27	chr2:55201200-55208000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:55201400-55208400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:55203800-55210000	Weak transcription	Ovary	ovary
30	chr2:55203800-55210800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
32	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
33	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
34	chr2:55204000-55208000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:55204000-55208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:55204200-55208600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:55204200-55214800	Strong transcription	Fetal Thymus	thymus
38	chr2:55204400-55208600	Weak transcription	Primary T cells from cord blood	blood
39	chr2:55204600-55208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:55204600-55209400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:55204600-55210600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:55204800-55208000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:55204800-55208200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:55204800-55208200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:55204800-55210400	Strong transcription	Osteobl	bone
46	chr2:55204800-55211600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:55205000-55211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:55205200-55208400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:55205200-55210600	Weak transcription	Aorta	Aorta
50	chr2:55205200-55210600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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