Variant report

Variant	rs1234424
Chromosome Location	chr2:148808770-148808771
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	chr2:148801657..148804409-chr2:148807658..148809416,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10171170	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10173542	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10180469	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10191634	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10497028	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497031	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10803524	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1227479	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1227482	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1227484	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1234398	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1234399	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234400	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1234403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234404	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234417	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1234420	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1234423	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1234426	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1234427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1234428	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234431	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17693310	0.87[ASN][1000 genomes]
rs1994189	0.95[ASN][1000 genomes]
rs4972323	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4972324	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59094777	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59984641	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60809905	0.88[ASN][1000 genomes]
rs60850392	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62169531	0.91[ASN][1000 genomes]
rs62169532	0.83[ASN][1000 genomes]
rs62169550	0.95[ASN][1000 genomes]
rs62183893	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183896	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183921	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183924	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62183925	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62183933	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6430280	0.87[ASN][1000 genomes]
rs6430293	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6430294	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6714702	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6750841	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7571453	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574172	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7602932	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv1005805	chr2:148755022-148842566	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv535976	chr2:148755022-148842566	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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
22	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
23	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
24	nsv1014570	chr2:148780080-148869729	Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv535978	chr2:148780080-148869729	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148779600-148844600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:148779800-148811600	Weak transcription	Placenta	Placenta
3	chr2:148779800-148814800	Weak transcription	Small Intestine	intestine
4	chr2:148779800-148825600	Weak transcription	Left Ventricle	heart
5	chr2:148780400-148809800	Weak transcription	Fetal Stomach	stomach
6	chr2:148781200-148814200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:148781600-148813400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:148781800-148810000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:148781800-148814800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:148781800-148822800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:148781800-148829600	Weak transcription	Fetal Intestine Small	intestine
12	chr2:148781800-148833400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:148784400-148811600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:148787200-148810400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:148791200-148818400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:148792200-148814000	Weak transcription	Pancreas	Pancrea
17	chr2:148795600-148843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:148796000-148816600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:148797000-148815200	Weak transcription	Liver	Liver
20	chr2:148798800-148813800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:148799200-148811400	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:148799200-148811600	Weak transcription	Fetal Thymus	thymus
23	chr2:148799200-148814000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:148799200-148827000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:148799400-148810000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:148799400-148814000	Weak transcription	Adipose Nuclei	Adipose
27	chr2:148799400-148839000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:148799400-148844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:148800000-148844600	Weak transcription	Fetal Lung	lung
30	chr2:148805200-148810200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:148805400-148809000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:148805600-148846200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:148805800-148809200	Flanking Active TSS	GM12878-XiMat	blood
34	chr2:148806600-148811600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:148806800-148811600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:148807000-148810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:148807000-148810400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:148807000-148811600	Weak transcription	Primary B cells from cord blood	blood
39	chr2:148807000-148811800	Weak transcription	HSMM	muscle
40	chr2:148807000-148812000	Weak transcription	Fetal Kidney	kidney
41	chr2:148807000-148813200	Weak transcription	Ovary	ovary
42	chr2:148807000-148814800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:148807000-148834000	Weak transcription	Brain Anterior Caudate	brain
44	chr2:148807000-148844600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:148807200-148810000	Weak transcription	HepG2	liver
46	chr2:148807200-148810200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:148807400-148814000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:148807400-148819000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:148807400-148833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:148807800-148812200	Weak transcription	H9 Cell Line	embryonic stem cell

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