Variant report

Variant	rs2298967
Chromosome Location	chr4:3185747-3185748
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	chr4:3110166..3112749-chr4:3184867..3187670,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs110501	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16843804	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16843836	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1891701	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2024115	1.00[CHB][hapmap]
rs2071655	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2071671	0.94[JPT][hapmap]
rs2157090	0.81[JPT][hapmap]
rs2269477	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269499	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2285086	1.00[CHB][hapmap]
rs2298971	0.93[ASN][1000 genomes]
rs2530601	0.81[JPT][hapmap]
rs2798221	0.90[JPT][hapmap]
rs28403215	0.93[ASN][1000 genomes]
rs3095077	0.90[JPT][hapmap]
rs3095081	1.00[YRI][hapmap]
rs3121419	0.95[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs362268	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs362271	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs362272	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs362273	0.95[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs362275	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs362296	0.84[JPT][hapmap]
rs362306	0.90[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs362309	0.81[ASN][1000 genomes]
rs362331	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs362336	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs363063	0.87[ASN][1000 genomes]
rs363064	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs363066	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs363088	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs363092	0.93[ASN][1000 genomes]
rs363096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs363099	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755883	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775061	0.80[EUR][1000 genomes]
rs3856973	0.94[CHB][hapmap]
rs4690011	0.91[ASN][1000 genomes]
rs4690072	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4690073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4690075	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59613878	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60197694	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61792530	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446723	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6446727	0.81[JPT][hapmap]
rs6446731	0.81[JPT][hapmap]
rs66684864	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6855981	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs73193303	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7659144	1.00[CHB][hapmap]
rs7661630	0.81[JPT][hapmap]
rs7685686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7691627	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs82332	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs82333	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs82334	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs916171	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9996868	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:3168000-3191800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr4:3168000-3192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
10	chr4:3171200-3186600	Strong transcription	GM12878-XiMat	blood
11	chr4:3171200-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:3171400-3187200	Strong transcription	Primary B cells from cord blood	blood
13	chr4:3171400-3192800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:3171600-3192800	Strong transcription	Primary T cells from cord blood	blood
15	chr4:3171600-3193600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:3172000-3192000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr4:3172200-3193000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:3172200-3195400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:3172400-3199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:3172600-3192400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:3173000-3192600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:3173000-3193000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:3173400-3188800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:3173600-3186800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:3173600-3187000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:3173600-3188000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:3173600-3192800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:3173600-3192800	Strong transcription	Placenta	Placenta
32	chr4:3173600-3193000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:3173600-3200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:3173800-3192800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:3173800-3192800	Strong transcription	Fetal Thymus	thymus
36	chr4:3173800-3193400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:3174000-3192600	Strong transcription	Thymus	Thymus
38	chr4:3174000-3192600	Strong transcription	Spleen	Spleen
39	chr4:3174000-3192800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:3174000-3192800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr4:3176400-3199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:3177000-3189600	Weak transcription	Fetal Heart	heart
44	chr4:3177000-3189800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:3177600-3189600	Weak transcription	Psoas Muscle	Psoas
46	chr4:3177800-3192600	Strong transcription	Left Ventricle	heart
47	chr4:3178400-3195200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr4:3178800-3200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr4:3179400-3192400	Strong transcription	Adipose Nuclei	Adipose
50	chr4:3179400-3192800	Strong transcription	Rectal Mucosa Donor 31	rectum

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