Variant report

Variant	rs62169550
Chromosome Location	chr2:148764045-148764046
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	chr2:148762250..148764768-chr2:148777590..148779447,2	MCF-7	breast:
2	chr2:148762432..148764977-chr2:148778675..148780305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204406	Chromatin interaction
ENSG00000115947	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10171170	0.81[ASN][1000 genomes]
rs10173542	0.90[ASN][1000 genomes]
rs10497028	0.87[ASN][1000 genomes]
rs10803524	0.91[ASN][1000 genomes]
rs1227479	0.87[ASN][1000 genomes]
rs1227482	0.91[ASN][1000 genomes]
rs1227484	0.90[ASN][1000 genomes]
rs1234398	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234399	0.84[ASN][1000 genomes]
rs1234400	0.82[ASN][1000 genomes]
rs1234403	0.95[ASN][1000 genomes]
rs1234404	0.84[ASN][1000 genomes]
rs1234414	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1234415	0.84[EUR][1000 genomes]
rs1234417	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234420	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234423	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234424	0.95[ASN][1000 genomes]
rs1234426	0.90[ASN][1000 genomes]
rs1234427	0.93[ASN][1000 genomes]
rs1234428	0.95[ASN][1000 genomes]
rs1234431	0.84[ASN][1000 genomes]
rs1234432	0.95[ASN][1000 genomes]
rs1424941	0.84[AMR][1000 genomes]
rs1469211	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17218938	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225402	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225423	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225430	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17232078	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17692648	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17693310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17743157	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1994189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754541	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3820715	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4972324	0.87[ASN][1000 genomes]
rs59094777	0.83[ASN][1000 genomes]
rs60809905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62169530	0.83[AMR][1000 genomes]
rs62169531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169532	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183893	0.87[ASN][1000 genomes]
rs62183896	0.83[ASN][1000 genomes]
rs62183921	0.83[ASN][1000 genomes]
rs6430280	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6430294	0.85[ASN][1000 genomes]
rs6714702	0.87[ASN][1000 genomes]
rs6750841	0.81[ASN][1000 genomes]
rs7571453	0.91[ASN][1000 genomes]
rs7574172	0.87[ASN][1000 genomes]
rs7602296	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs981814	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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
26	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
27	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
28	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
29	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
30	esv3361276	chr2:148756269-148781613	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription 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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148694200-148777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:148709400-148776800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:148728200-148773400	Weak transcription	K562	blood
4	chr2:148736000-148776800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:148736400-148765600	Weak transcription	A549	lung
6	chr2:148748000-148771400	Weak transcription	Fetal Kidney	kidney
7	chr2:148753400-148764400	Weak transcription	Primary B cells from cord blood	blood
8	chr2:148753400-148764600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:148753400-148765200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:148753400-148765800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:148753400-148775800	Weak transcription	Thymus	Thymus
12	chr2:148753400-148776400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:148753400-148776400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:148753400-148777600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:148754000-148765000	Weak transcription	Fetal Intestine Large	intestine
16	chr2:148754600-148764200	Weak transcription	HepG2	liver
17	chr2:148755000-148764200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:148756000-148764200	Weak transcription	Right Atrium	heart
19	chr2:148756400-148768800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:148757200-148764200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:148757200-148764200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:148757200-148770400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:148757200-148777600	Weak transcription	Small Intestine	intestine
24	chr2:148757600-148776200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:148758400-148764200	Weak transcription	Pancreas	Pancrea
26	chr2:148758600-148764200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:148758600-148774200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:148758800-148775400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:148759000-148764200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:148759000-148775400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:148759400-148775400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:148761200-148764400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:148761400-148772200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:148762200-148764600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:148762600-148766400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:148762800-148764600	ZNF genes & repeats	Fetal Stomach	stomach
37	chr2:148763200-148764600	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr2:148763200-148764800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr2:148763400-148764600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:148763400-148764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:148763600-148764200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr2:148763600-148764400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:148763600-148764400	Enhancers	Spleen	Spleen
44	chr2:148763600-148764600	Enhancers	Psoas Muscle	Psoas
45	chr2:148763600-148764800	Strong transcription	Primary T cells from cord blood	blood
46	chr2:148763800-148764400	Enhancers	Esophagus	oesophagus
47	chr2:148763800-148764600	Enhancers	Lung	lung
48	chr2:148763800-148764800	Enhancers	Liver	Liver
49	chr2:148763800-148764800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:148763800-148773400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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