Variant report

Variant	rs7520255
Chromosome Location	chr1:78447822-78447823
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	chr1:78447431..78449969-chr1:78468449..78471656,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB4-1	chr1:78444779-78456066	NONHSAT004062

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1039863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10735751	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10873961	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873962	0.84[ASN][1000 genomes]
rs10873963	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11162401	0.92[ASN][1000 genomes]
rs1166696	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1166699	0.90[ASN][1000 genomes]
rs1166700	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11805942	0.92[ASN][1000 genomes]
rs11806130	0.94[ASN][1000 genomes]
rs11811805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1510244	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17101101	0.92[ASN][1000 genomes]
rs1749911	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1749913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1780044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1780045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1780047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1780048	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1780052	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2296452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3736909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3767024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3767025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4083559	0.89[ASN][1000 genomes]
rs4107671	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4483454	0.90[ASN][1000 genomes]
rs4543852	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4631748	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949823	0.83[CHB][hapmap]
rs6424648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6424653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6604878	0.82[CHB][hapmap]
rs6675105	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6680447	0.93[ASN][1000 genomes]
rs6699513	0.84[ASN][1000 genomes]
rs6702465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72685363	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685364	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72685368	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7523874	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7524504	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547599	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9661687	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9662129	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9729146	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78445800-78449600	Weak transcription	Stomach Mucosa	stomach
2	chr1:78445800-78449800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:78446000-78448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:78446000-78448200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:78446000-78449800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:78446000-78449800	Weak transcription	Small Intestine	intestine
7	chr1:78446000-78451800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:78446000-78452600	Weak transcription	Gastric	stomach
9	chr1:78446000-78455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:78446000-78458600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:78446000-78458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:78446000-78461000	Weak transcription	Placenta	Placenta
13	chr1:78446200-78448400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:78446200-78449400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:78446200-78451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:78446200-78452400	Weak transcription	Psoas Muscle	Psoas
17	chr1:78446200-78452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:78446200-78457200	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:78446200-78461200	Weak transcription	Fetal Stomach	stomach
20	chr1:78446200-78469600	Weak transcription	Thymus	Thymus
21	chr1:78446400-78448000	Enhancers	Brain Hippocampus Middle	brain
22	chr1:78446400-78451800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:78446400-78458200	Weak transcription	Fetal Thymus	thymus
24	chr1:78446400-78469800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:78446400-78470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:78446600-78448000	Enhancers	Dnd41	blood
27	chr1:78446600-78448200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:78446600-78449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:78446600-78449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:78446600-78449600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:78446600-78449600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:78446600-78449600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:78446600-78449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:78446600-78450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:78446600-78450000	Weak transcription	Fetal Heart	heart
36	chr1:78446600-78450600	Weak transcription	HSMMtube	muscle
37	chr1:78446600-78450800	Weak transcription	Primary B cells from cord blood	blood
38	chr1:78446600-78450800	Enhancers	HepG2	liver
39	chr1:78446600-78451800	Weak transcription	Right Atrium	heart
40	chr1:78446600-78457200	Weak transcription	Primary T cells from cord blood	blood
41	chr1:78446600-78459200	Weak transcription	Fetal Brain Female	brain
42	chr1:78446600-78460800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:78446600-78461200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:78446600-78468000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:78446600-78468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:78446600-78468800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:78446600-78468800	Weak transcription	Adipose Nuclei	Adipose
48	chr1:78446600-78468800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:78446600-78469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:78446600-78469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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