Variant report

Variant	rs6884370
Chromosome Location	chr5:52163352-52163353
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52159091..52161202-chr5:52161299..52164243,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213949	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10038615	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10046016	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10513000	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10513001	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11949835	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11952083	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11956627	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12110170	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1478445	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16880353	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59192299	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60422098	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6860395	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6880226	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886404	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6894627	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6895807	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6896699	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73102285	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73754051	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73754052	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73754053	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73754054	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73754055	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73754057	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73756267	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73756268	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73756272	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7704305	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1032554	chr5:52126688-52174119	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52142000-52220200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:52142200-52166400	Weak transcription	Spleen	Spleen
3	chr5:52143600-52173600	Weak transcription	Left Ventricle	heart
4	chr5:52145800-52181000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:52146800-52166000	Weak transcription	HepG2	liver
6	chr5:52150200-52166400	Weak transcription	Fetal Intestine Small	intestine
7	chr5:52153200-52163400	Weak transcription	Dnd41	blood
8	chr5:52153200-52166400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:52154000-52164200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:52154200-52166400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:52155800-52163600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:52156000-52166400	Weak transcription	Lung	lung
13	chr5:52156000-52180400	Weak transcription	Placenta	Placenta
14	chr5:52156200-52166000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:52157400-52166200	Weak transcription	NHEK	skin
16	chr5:52157600-52166200	Weak transcription	Aorta	Aorta
17	chr5:52158400-52176800	Weak transcription	Primary T cells from cord blood	blood
18	chr5:52159800-52166400	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:52159800-52166400	Weak transcription	Small Intestine	intestine
20	chr5:52159800-52191800	Weak transcription	Pancreas	Pancrea
21	chr5:52160200-52166200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:52160400-52164400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:52160600-52163600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:52160600-52166000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:52160600-52166000	Weak transcription	HMEC	breast
26	chr5:52160800-52165000	Strong transcription	Liver	Liver
27	chr5:52160800-52165400	Weak transcription	Fetal Kidney	kidney
28	chr5:52160800-52166000	Weak transcription	Osteobl	bone
29	chr5:52161000-52163800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:52161000-52165400	Weak transcription	Fetal Lung	lung
31	chr5:52161000-52165400	Weak transcription	NHDF-Ad	bronchial
32	chr5:52161000-52166200	Weak transcription	HSMM	muscle
33	chr5:52161000-52166400	Weak transcription	NH-A	brain
34	chr5:52161000-52172600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:52161000-52183200	Weak transcription	Fetal Stomach	stomach
36	chr5:52161000-52191000	Weak transcription	Ovary	ovary
37	chr5:52161200-52165800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:52161400-52163400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr5:52161400-52165000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:52161400-52166000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:52161600-52164400	Weak transcription	Adipose Nuclei	Adipose
42	chr5:52161600-52166400	Weak transcription	NHLF	lung
43	chr5:52161800-52166000	Weak transcription	HSMMtube	muscle
44	chr5:52162000-52164800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:52162400-52165600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr5:52163000-52165800	Weak transcription	Fetal Intestine Large	intestine
47	chr5:52163200-52163800	Enhancers	Colon Smooth Muscle	Colon
48	chr5:52163200-52164800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:52163200-52165000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:52163200-52165200	Enhancers	Right Atrium	heart

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