Variant report

Variant	rs2100469
Chromosome Location	chr2:148746693-148746694
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	chr2:148746466..148747928-chr2:148959011..148960040,7	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10180655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10209751	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10439198	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10439199	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10928374	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10928375	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10928377	0.85[ASN][1000 genomes]
rs10928378	0.82[ASN][1000 genomes]
rs11676430	0.86[EUR][1000 genomes]
rs11685710	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12105745	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1227304	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1234396	1.00[ASN][1000 genomes]
rs1234397	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234402	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234405	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234410	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234413	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234418	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234429	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234430	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234433	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1238800	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12472291	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12615059	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12622150	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs13016893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1312025	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13395141	0.80[EUR][1000 genomes]
rs13398026	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13411680	0.86[ASN][1000 genomes]
rs13430086	0.83[CEU][hapmap]
rs1375859	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1377454	0.86[EUR][1000 genomes]
rs1449958	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1597406	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1872198	1.00[ASN][1000 genomes]
rs1895694	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1901013	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2113792	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2194695	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2288190	0.81[YRI][hapmap]
rs2382202	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603597	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2603599	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603600	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2627019	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2627025	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28475125	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28870981	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2890922	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768684	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3768686	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3768688	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3820716	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4419186	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6430287	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6430288	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6430291	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6430298	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6709182	0.89[CEU][hapmap];0.87[YRI][hapmap]
rs6713811	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6727415	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6731371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6753116	0.87[EUR][1000 genomes]
rs73005159	0.89[ASN][1000 genomes]
rs7422771	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7423983	0.85[EUR][1000 genomes]
rs7558404	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7566230	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7568722	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7569629	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577025	1.00[ASN][1000 genomes]
rs7580420	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7580610	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7582403	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7587464	0.87[EUR][1000 genomes]
rs7593570	0.84[ASN][1000 genomes]
rs7595938	0.93[ASN][1000 genomes]
rs9287411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs979636	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS 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
6	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers 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
8	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
9	nsv1004169	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv535970	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv869326	chr2:148727068-148859804	Weak transcription Flanking Active TSS Enhancers Strong 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	9 gene(s)	inside rSNPs	diseases
14	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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
16	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription 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
17	nsv1009807	chr2:148731025-148829378	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats 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
18	nsv535973	chr2:148731025-148829378	Flanking Active TSS Strong transcription Weak transcription Enhancers 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	9 gene(s)	inside rSNPs	diseases
19	nsv1009696	chr2:148739650-148805668	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv535974	chr2:148739650-148805668	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats 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
21	nsv1011381	chr2:148739850-148805529	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv535975	chr2:148739850-148805529	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv999777	chr2:148740742-148809464	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
24	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
25	nsv1015003	chr2:148745734-148839653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2100469	ORC4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148694200-148777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:148695000-148746800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:148709200-148747600	Weak transcription	Adipose Nuclei	Adipose
5	chr2:148709400-148776800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:148709800-148747000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:148721400-148752800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:148721400-148763600	Weak transcription	Spleen	Spleen
9	chr2:148722800-148756400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:148725600-148747600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:148726400-148752600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:148726600-148746800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:148726600-148752600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:148728200-148773400	Weak transcription	K562	blood
15	chr2:148730800-148752600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:148731000-148746800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:148731400-148752800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:148736000-148776800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:148736200-148747000	Weak transcription	Left Ventricle	heart
20	chr2:148736200-148752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:148736200-148752400	Weak transcription	Fetal Intestine Small	intestine
22	chr2:148736200-148752600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:148736200-148752800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:148736400-148747600	Weak transcription	Fetal Kidney	kidney
25	chr2:148736400-148750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:148736400-148750400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:148736400-148750600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:148736400-148765600	Weak transcription	A549	lung
29	chr2:148736600-148752600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:148736600-148752600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:148737000-148753200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:148737600-148747600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:148737600-148747800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:148737600-148752600	Weak transcription	Primary B cells from cord blood	blood
35	chr2:148737600-148752600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:148739000-148750400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:148739000-148752600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:148739000-148759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:148741200-148747200	Weak transcription	Fetal Lung	lung
40	chr2:148741200-148758000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:148741600-148755800	Weak transcription	Ovary	ovary
42	chr2:148741600-148756200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:148741800-148752800	Weak transcription	Thymus	Thymus
44	chr2:148741800-148757400	Weak transcription	Aorta	Aorta
45	chr2:148742200-148755800	Weak transcription	Gastric	stomach
46	chr2:148742400-148747600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:148742400-148755800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:148742400-148756000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr2:148742600-148747600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:148742800-148752800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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