Variant report

Variant	rs2248228
Chromosome Location	chr3:45965386-45965387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45943266..45944977-chr3:45963147..45965893,2	MCF-7	breast:
2	chr3:45952412..45954426-chr3:45964464..45966839,2	K562	blood:

Variant related genes	Relation type
ENSG00000201635	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1072755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130080	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12495073	0.96[CEU][hapmap]
rs12630101	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12635494	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12635657	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12639598	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13066048	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13073861	0.92[CEU][hapmap]
rs13091821	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13091979	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1532071	0.88[ASN][1000 genomes]
rs1552489	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552490	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1601867	0.86[ASN][1000 genomes]
rs17078449	0.86[CHB][hapmap]
rs1994488	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1994489	0.88[ASN][1000 genomes]
rs2054866	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2131091	0.92[CEU][hapmap]
rs2171530	0.94[ASN][1000 genomes]
rs2234358	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2291470	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35465473	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733103	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774634	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774635	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774638	0.82[CHB][hapmap]
rs3774639	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796373	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3796375	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs3821884	0.82[CHB][hapmap]
rs4535265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4682799	0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4682800	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs4683147	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683148	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683149	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683152	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683154	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683156	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6778896	0.81[EUR][1000 genomes]
rs6781121	0.89[CHB][hapmap]
rs6800954	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7129	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs730983	1.00[CEU][hapmap]
rs737452	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs751552	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs751553	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs9311380	0.88[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936939	0.81[CHB][hapmap]
rs9824253	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking 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	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr3:45957800-45969000	Weak transcription	K562	blood
2	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:45958000-45969000	Weak transcription	NH-A	brain
4	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach
6	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
7	chr3:45958600-45968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:45958600-45970000	Weak transcription	Small Intestine	intestine
9	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
12	chr3:45959000-45966000	Genic enhancers	Fetal Thymus	thymus
13	chr3:45959000-45973600	Weak transcription	Fetal Kidney	kidney
14	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:45959400-45965800	Genic enhancers	Thymus	Thymus
17	chr3:45959400-45965800	Genic enhancers	Dnd41	blood
18	chr3:45959400-45966000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:45959400-45971800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:45959400-45973400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:45959600-45965600	Strong transcription	Brain Cingulate Gyrus	brain
23	chr3:45959600-45973200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:45959800-45965600	Weak transcription	Hela-S3	cervix
25	chr3:45959800-45974600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:45959800-45979800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:45959800-45979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:45960000-45965800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:45960000-45965800	Strong transcription	Adipose Nuclei	Adipose
31	chr3:45960000-45966000	Strong transcription	Liver	Liver
32	chr3:45960000-45966200	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:45960000-45967800	Strong transcription	Placenta	Placenta
34	chr3:45960000-45979400	Strong transcription	Fetal Intestine Large	intestine
35	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:45960200-45965800	Strong transcription	Esophagus	oesophagus
37	chr3:45960200-45965800	Strong transcription	Spleen	Spleen
38	chr3:45960200-45966000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:45960200-45966000	Strong transcription	Lung	lung
40	chr3:45960200-45966000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:45960200-45974200	Strong transcription	Fetal Intestine Small	intestine
42	chr3:45960400-45965800	Strong transcription	Primary B cells from cord blood	blood
43	chr3:45960400-45965800	Strong transcription	Pancreas	Pancrea
44	chr3:45960400-45966000	Strong transcription	Aorta	Aorta
45	chr3:45960400-45966000	Strong transcription	Ovary	ovary
46	chr3:45960400-45969000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:45960400-45980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:45960800-45966000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:45960800-45966000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:45960800-45966200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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