Variant report

Variant	rs10205246
Chromosome Location	chr2:148939578-148939579
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	chr2:148924504..148926944-chr2:148937289..148939887,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10209751	0.93[ASN][1000 genomes]
rs10439198	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10439199	0.89[ASN][1000 genomes]
rs10928374	0.80[ASN][1000 genomes]
rs10928375	0.91[ASN][1000 genomes]
rs10928377	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10928378	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11676430	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685710	0.92[ASN][1000 genomes]
rs1234402	0.86[ASN][1000 genomes]
rs1234405	0.86[ASN][1000 genomes]
rs1234410	0.86[ASN][1000 genomes]
rs1234413	0.88[ASN][1000 genomes]
rs1234416	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1234418	0.81[ASN][1000 genomes]
rs1234429	0.85[ASN][1000 genomes]
rs1234430	0.86[ASN][1000 genomes]
rs1234433	0.86[ASN][1000 genomes]
rs1238800	0.88[ASN][1000 genomes]
rs12472291	0.80[ASN][1000 genomes]
rs12479178	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615059	0.89[ASN][1000 genomes]
rs1312025	0.86[ASN][1000 genomes]
rs13395141	0.88[ASN][1000 genomes]
rs13398026	0.93[ASN][1000 genomes]
rs13411680	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1375859	0.91[ASN][1000 genomes]
rs1449958	0.88[ASN][1000 genomes]
rs1597406	0.91[ASN][1000 genomes]
rs1901013	0.97[ASN][1000 genomes]
rs28475125	0.93[ASN][1000 genomes]
rs28870981	0.93[ASN][1000 genomes]
rs2890922	0.92[ASN][1000 genomes]
rs6430287	0.89[ASN][1000 genomes]
rs6430288	0.89[ASN][1000 genomes]
rs6430291	0.88[ASN][1000 genomes]
rs6430298	0.93[ASN][1000 genomes]
rs6727415	0.92[ASN][1000 genomes]
rs7422771	0.93[ASN][1000 genomes]
rs7423983	0.87[ASN][1000 genomes]
rs7558404	0.93[ASN][1000 genomes]
rs7568722	0.91[ASN][1000 genomes]
rs7569629	0.91[ASN][1000 genomes]
rs7580420	0.91[ASN][1000 genomes]
rs7580610	0.91[ASN][1000 genomes]
rs7587464	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595938	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979636	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
14	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10205246	ORC4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 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	chr2:148919800-148945800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:148924200-148941800	Weak transcription	Brain Angular Gyrus	brain
5	chr2:148924400-148946400	Weak transcription	HSMMtube	muscle
6	chr2:148924600-148946800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:148925200-148959000	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:148927000-148940400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:148927200-148942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:148927400-148942000	Weak transcription	HMEC	breast
11	chr2:148928200-148945400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:148928400-148943800	Weak transcription	Fetal Brain Female	brain
13	chr2:148928400-148944600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:148928600-148993600	Weak transcription	HSMM	muscle
15	chr2:148928800-148945600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:148929400-148941000	Weak transcription	NHLF	lung
17	chr2:148929600-148944800	Weak transcription	Osteobl	bone
18	chr2:148929800-148944400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:148929800-148960800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:148930600-148946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:148930800-148948200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:148931000-148942400	Weak transcription	Fetal Stomach	stomach
23	chr2:148931000-148942600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:148931000-148960600	Weak transcription	Spleen	Spleen
25	chr2:148931200-148939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:148931200-148942200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:148931200-148944200	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:148931200-148948400	Weak transcription	Pancreas	Pancrea
29	chr2:148931200-148958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:148931200-148993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:148933800-148942400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:148933800-148953400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:148934200-148943400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:148934400-148942200	Weak transcription	Placenta	Placenta
35	chr2:148934400-148943600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:148934600-148942400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:148934600-148943800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:148934600-148943800	Weak transcription	Liver	Liver
39	chr2:148935000-148940400	Weak transcription	Psoas Muscle	Psoas
40	chr2:148935400-148940200	Weak transcription	GM12878-XiMat	blood
41	chr2:148935400-148942200	Weak transcription	Dnd41	blood
42	chr2:148935400-148944400	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:148935400-148946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:148935600-148943800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:148935600-148945000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:148935600-148945400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:148935600-148946000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:148935600-148946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:148935800-148940400	Weak transcription	NHDF-Ad	bronchial
50	chr2:148935800-148945400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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