Variant report

Variant	rs1377454
Chromosome Location	chr2:148937370-148937371
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	chr2:148924504..148926944-chr2:148937289..148939887,2	MCF-7	breast:
2	chr2:148931889..148933794-chr2:148936353..148939104,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10209751	0.93[EUR][1000 genomes]
rs10439198	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10439199	0.92[EUR][1000 genomes]
rs10928374	0.87[EUR][1000 genomes]
rs10928375	0.92[EUR][1000 genomes]
rs11676430	0.98[EUR][1000 genomes]
rs11685710	0.93[EUR][1000 genomes]
rs1234397	0.86[EUR][1000 genomes]
rs1234402	0.84[EUR][1000 genomes]
rs1234405	0.87[EUR][1000 genomes]
rs1234410	0.85[EUR][1000 genomes]
rs1234413	0.87[EUR][1000 genomes]
rs1234416	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1234418	0.88[EUR][1000 genomes]
rs1234429	0.83[EUR][1000 genomes]
rs1234430	0.88[EUR][1000 genomes]
rs1234433	0.83[EUR][1000 genomes]
rs1238800	0.83[EUR][1000 genomes]
rs12472291	0.89[EUR][1000 genomes]
rs12615059	0.87[EUR][1000 genomes]
rs1312025	0.89[EUR][1000 genomes]
rs13395141	0.92[EUR][1000 genomes]
rs13398026	0.90[EUR][1000 genomes]
rs1375859	0.88[EUR][1000 genomes]
rs1449958	0.87[EUR][1000 genomes]
rs1597406	0.87[EUR][1000 genomes]
rs1901013	0.95[EUR][1000 genomes]
rs2100469	0.86[EUR][1000 genomes]
rs2382202	0.83[EUR][1000 genomes]
rs2603599	0.83[EUR][1000 genomes]
rs28475125	0.90[EUR][1000 genomes]
rs28870981	0.90[EUR][1000 genomes]
rs2890922	0.87[EUR][1000 genomes]
rs6430287	0.87[EUR][1000 genomes]
rs6430288	0.87[EUR][1000 genomes]
rs6430291	0.89[EUR][1000 genomes]
rs6430298	0.90[EUR][1000 genomes]
rs6727415	0.88[EUR][1000 genomes]
rs6753116	0.87[EUR][1000 genomes]
rs7422771	0.94[EUR][1000 genomes]
rs7423983	0.86[EUR][1000 genomes]
rs7558404	0.88[EUR][1000 genomes]
rs7568722	0.90[EUR][1000 genomes]
rs7569629	0.86[EUR][1000 genomes]
rs7580420	0.89[EUR][1000 genomes]
rs7580610	0.87[EUR][1000 genomes]
rs7587464	0.99[EUR][1000 genomes]
rs979636	0.86[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	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv997674	chr2:148862630-148995570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1007998	chr2:148866051-148995570	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv999952	chr2:148884787-148938697	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv915953	chr2:148934787-148977722	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1377454	ORC4L	Cis_1M	lymphoblastoid	RTeQTL
rs1377454	ACVR2A	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148911400-148942400	Weak transcription	Ovary	ovary
2	chr2:148913000-148977600	Weak transcription	Aorta	Aorta
3	chr2:148916800-148938600	Weak transcription	Primary B cells from cord blood	blood
4	chr2:148918800-148938000	Weak transcription	Fetal Lung	lung
5	chr2:148919800-148945800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:148924200-148941800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:148924400-148938000	Weak transcription	Fetal Kidney	kidney
8	chr2:148924400-148946400	Weak transcription	HSMMtube	muscle
9	chr2:148924600-148946800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:148925200-148959000	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:148926000-148938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:148927000-148940400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:148927200-148942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:148927400-148942000	Weak transcription	HMEC	breast
15	chr2:148928200-148945400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:148928400-148943800	Weak transcription	Fetal Brain Female	brain
17	chr2:148928400-148944600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:148928600-148993600	Weak transcription	HSMM	muscle
19	chr2:148928800-148945600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:148929000-148937800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:148929400-148941000	Weak transcription	NHLF	lung
22	chr2:148929600-148944800	Weak transcription	Osteobl	bone
23	chr2:148929800-148944400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:148929800-148960800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:148930000-148938000	Weak transcription	Left Ventricle	heart
26	chr2:148930600-148946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:148930800-148948200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:148931000-148937800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:148931000-148938000	Weak transcription	Thymus	Thymus
30	chr2:148931000-148942400	Weak transcription	Fetal Stomach	stomach
31	chr2:148931000-148942600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:148931000-148960600	Weak transcription	Spleen	Spleen
33	chr2:148931200-148939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:148931200-148942200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:148931200-148944200	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:148931200-148948400	Weak transcription	Pancreas	Pancrea
37	chr2:148931200-148958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:148931200-148993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:148933800-148942400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:148933800-148953400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:148934200-148943400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:148934400-148942200	Weak transcription	Placenta	Placenta
43	chr2:148934400-148943600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr2:148934600-148942400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr2:148934600-148943800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:148934600-148943800	Weak transcription	Liver	Liver
47	chr2:148935000-148940400	Weak transcription	Psoas Muscle	Psoas
48	chr2:148935400-148940200	Weak transcription	GM12878-XiMat	blood
49	chr2:148935400-148942200	Weak transcription	Dnd41	blood
50	chr2:148935400-148944400	Weak transcription	Colon Smooth Muscle	Colon

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