Variant report

Variant	rs1554257
Chromosome Location	chr4:48761896-48761897
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	chr4:48756947..48759205-chr4:48760988..48763771,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10029425	1.00[AMR][1000 genomes]
rs10034207	0.92[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049760	0.92[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10805171	1.00[AMR][1000 genomes]
rs10805172	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10938535	1.00[AMR][1000 genomes]
rs10938538	1.00[AMR][1000 genomes]
rs10938539	1.00[AMR][1000 genomes]
rs10938541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12500224	1.00[AMR][1000 genomes]
rs12500244	1.00[AMR][1000 genomes]
rs12507475	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12507546	1.00[AMR][1000 genomes]
rs1474072	1.00[AMR][1000 genomes]
rs1517673	1.00[AMR][1000 genomes]
rs1517676	1.00[AMR][1000 genomes]
rs1517677	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1533511	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1616561	1.00[AMR][1000 genomes]
rs1702796	1.00[AMR][1000 genomes]
rs1702799	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1712762	1.00[YRI][hapmap]
rs1712771	1.00[AMR][1000 genomes]
rs1949422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2138866	0.92[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2138867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2354939	0.82[YRI][hapmap]
rs2572342	0.82[YRI][hapmap]
rs28371079	1.00[AMR][1000 genomes]
rs2883410	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2940319	0.92[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4235155	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4235157	1.00[AMR][1000 genomes]
rs4330326	1.00[AMR][1000 genomes]
rs4558842	1.00[AMR][1000 genomes]
rs4694896	1.00[AMR][1000 genomes]
rs4694898	1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	1.00[AMR][1000 genomes]
rs4695386	1.00[AMR][1000 genomes]
rs4695390	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4695402	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs4695406	0.82[YRI][hapmap]
rs6447642	1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6821456	1.00[AMR][1000 genomes]
rs6823351	1.00[AMR][1000 genomes]
rs6827481	1.00[AMR][1000 genomes]
rs6828500	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835757	1.00[AMR][1000 genomes]
rs6839713	1.00[YRI][hapmap]
rs6844088	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6846797	1.00[AMR][1000 genomes]
rs6848222	1.00[AMR][1000 genomes]
rs6848417	1.00[AMR][1000 genomes]
rs6853876	1.00[AMR][1000 genomes]
rs707720	1.00[AMR][1000 genomes]
rs7434721	1.00[AMR][1000 genomes]
rs7664507	1.00[AMR][1000 genomes]
rs7667909	0.87[ASW][hapmap]
rs7689293	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7689662	1.00[AMR][1000 genomes]
rs7692480	1.00[AMR][1000 genomes]
rs7698064	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776581	0.85[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs776583	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs776587	1.00[AMR][1000 genomes]
rs776589	1.00[AMR][1000 genomes]
rs776595	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs776603	1.00[AMR][1000 genomes]
rs938789	0.83[AFR][1000 genomes]
rs938791	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9994214	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998178	1.00[YRI][hapmap];1.00[AMR][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	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv594137	chr4:48748305-48763163	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48742000-48768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:48742600-48768200	Weak transcription	Pancreas	Pancrea
4	chr4:48745000-48765200	Weak transcription	Primary B cells from cord blood	blood
5	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
6	chr4:48747400-48767800	Weak transcription	Fetal Intestine Large	intestine
7	chr4:48749200-48768200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:48751000-48768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:48751800-48763800	Weak transcription	Spleen	Spleen
11	chr4:48751800-48763800	Weak transcription	HSMM	muscle
12	chr4:48752000-48762600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:48752000-48767000	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:48752400-48765200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:48753200-48764600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:48754400-48763800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:48754600-48768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:48755000-48763400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:48755000-48767400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
22	chr4:48755200-48763000	Weak transcription	Psoas Muscle	Psoas
23	chr4:48755200-48763800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:48755200-48765200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:48755200-48765400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:48755200-48768400	Weak transcription	Fetal Thymus	thymus
27	chr4:48755200-48769400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr4:48755200-48774200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:48755400-48763600	Weak transcription	Osteobl	bone
30	chr4:48755400-48763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:48755400-48763800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:48755400-48768200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:48755400-48775600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:48755600-48774800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:48756000-48764200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:48756000-48773000	Weak transcription	HUVEC	blood vessel
37	chr4:48756000-48774800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:48756200-48764400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:48756200-48774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:48756600-48768600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:48756600-48769600	Weak transcription	Primary T cells from cord blood	blood
42	chr4:48757800-48763600	Weak transcription	Brain Anterior Caudate	brain
43	chr4:48758600-48763000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:48758800-48763000	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:48759000-48763000	Weak transcription	Fetal Heart	heart
46	chr4:48759000-48763800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:48759000-48763800	Weak transcription	Right Ventricle	heart
48	chr4:48759000-48765200	Weak transcription	Lung	lung
49	chr4:48759000-48768200	Weak transcription	Brain Substantia Nigra	brain
50	chr4:48759000-48775600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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