Variant report

Variant	rs10517689
Chromosome Location	chr4:159101786-159101787
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159096212..159097813-chr4:159101529..159103771,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248429	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10005007	0.93[ASN][1000 genomes]
rs10007737	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008208	1.00[JPT][hapmap]
rs10012339	1.00[JPT][hapmap]
rs10018872	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10024133	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10026876	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028490	1.00[JPT][hapmap]
rs11100150	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11100151	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11937022	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938464	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12502811	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12511679	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645131	1.00[JPT][hapmap]
rs12648410	1.00[JPT][hapmap]
rs13113959	0.90[AMR][1000 genomes]
rs1320370	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320371	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14202	1.00[JPT][hapmap]
rs17036927	1.00[CEU][hapmap]
rs2346319	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2346320	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346321	1.00[JPT][hapmap]
rs2346381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346774	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2346776	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346780	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346783	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346784	1.00[JPT][hapmap]
rs28499342	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28691778	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28719822	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881373	1.00[JPT][hapmap]
rs2881473	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4234917	1.00[JPT][hapmap]
rs4317248	1.00[JPT][hapmap]
rs4324593	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4345228	1.00[JPT][hapmap]
rs4391084	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472184	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4501266	1.00[JPT][hapmap]
rs4582199	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4627913	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4690893	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691455	1.00[JPT][hapmap]
rs4691456	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4691457	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4691458	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4691459	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691461	1.00[JPT][hapmap]
rs4691462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691464	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691465	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691467	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6536299	1.00[JPT][hapmap]
rs6812635	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813306	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819576	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820988	1.00[JPT][hapmap]
rs6821598	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6830702	1.00[JPT][hapmap]
rs6832099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833198	1.00[JPT][hapmap]
rs6834164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6849902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6855420	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671501	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7686997	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180159	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8370	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159092600-159104000	Weak transcription	Lung	lung
2	chr4:159094400-159103200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:159095000-159103200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:159095800-159113800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:159096200-159103200	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:159096400-159107400	Weak transcription	HSMMtube	muscle
7	chr4:159096400-159113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:159096400-159131200	Weak transcription	Right Ventricle	heart
9	chr4:159096400-159131200	Weak transcription	HepG2	liver
10	chr4:159097800-159103200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:159097800-159103200	Weak transcription	Left Ventricle	heart
12	chr4:159097800-159122400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:159098000-159102200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:159098400-159103200	Weak transcription	Brain Angular Gyrus	brain
15	chr4:159098400-159103200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:159098400-159110200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:159098400-159122800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:159098800-159122800	Weak transcription	Fetal Intestine Large	intestine
19	chr4:159099000-159104000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:159099600-159112800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:159099800-159107400	Weak transcription	Adipose Nuclei	Adipose
22	chr4:159099800-159114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:159099800-159131200	Weak transcription	HSMM	muscle
24	chr4:159099800-159131400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:159100000-159108600	Weak transcription	Ovary	ovary
26	chr4:159100200-159103400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:159100200-159120200	Weak transcription	Aorta	Aorta
28	chr4:159100600-159103200	Weak transcription	Brain Substantia Nigra	brain
29	chr4:159100600-159106200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:159100800-159102200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:159101000-159102600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:159101000-159102600	Weak transcription	HMEC	breast
33	chr4:159101200-159103200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:159101200-159103200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:159101600-159130400	Weak transcription	HUVEC	blood vessel

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