Variant report

Variant	rs6587841
Chromosome Location	chr1:59370906-59370907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59348233..59353011-chr1:59368695..59371190,6	K562	blood:
2	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
3	chr1:59363087..59366662-chr1:59367277..59371776,8	K562	blood:
4	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
5	chr1:59368962..59371702-chr1:59384536..59386461,2	MCF-7	breast:
6	chr1:59248088..59252183-chr1:59365231..59372787,10	MCF-7	breast:
7	chr1:59370025..59373918-chr1:59374367..59377851,5	K562	blood:
8	chr1:59247507..59253331-chr1:59366916..59371031,9	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JUN-12	chr1:59370196-59371006	NONHSAT003541
2	lnc-JUN-12	chr1:59370774-59371006	NONHSAT003542
3	lnc-JUN-12	chr1:59370198-59371006	refGeneNc_2716_NR_027120

No data

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493253	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207323	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11207325	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11207326	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11207332	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12117564	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12404569	0.80[EUR][1000 genomes]
rs12409909	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17118379	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057596	0.85[AMR][1000 genomes]
rs2953373	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41287666	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658104	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6661505	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6664131	0.87[EUR][1000 genomes]
rs6681632	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697107	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74078024	0.88[EUR][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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59369800-59388200	Weak transcription	Gastric	stomach
2	chr1:59370000-59371400	Enhancers	Stomach Mucosa	stomach
3	chr1:59370000-59371600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:59370000-59372200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:59370000-59373200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:59370000-59377800	Weak transcription	Aorta	Aorta
7	chr1:59370200-59371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:59370200-59371000	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:59370200-59371000	Enhancers	Duodenum Mucosa	Duodenum
10	chr1:59370200-59371000	Enhancers	Fetal Intestine Large	intestine
11	chr1:59370200-59371000	Enhancers	Spleen	Spleen
12	chr1:59370200-59371200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:59370200-59371400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:59370200-59371400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:59370200-59371400	Weak transcription	Brain Germinal Matrix	brain
16	chr1:59370200-59371400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:59370200-59371400	Enhancers	HUVEC	blood vessel
18	chr1:59370200-59371600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:59370200-59371600	Enhancers	Brain Angular Gyrus	brain
20	chr1:59370200-59371600	Enhancers	K562	blood
21	chr1:59370200-59371600	Enhancers	NHDF-Ad	bronchial
22	chr1:59370200-59371800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:59370200-59371800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:59370200-59371800	Enhancers	Fetal Intestine Small	intestine
25	chr1:59370200-59372000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:59370200-59372200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:59370200-59372400	Weak transcription	Colonic Mucosa	Colon
28	chr1:59370200-59372400	Enhancers	HepG2	liver
29	chr1:59370200-59373200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:59370200-59373600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:59370200-59374000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:59370200-59374200	Weak transcription	HSMM	muscle
33	chr1:59370200-59374200	Weak transcription	HSMMtube	muscle
34	chr1:59370200-59374200	Weak transcription	Osteobl	bone
35	chr1:59370200-59374400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:59370200-59374400	Weak transcription	Psoas Muscle	Psoas
37	chr1:59370200-59374400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:59370200-59375200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:59370200-59377200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:59370200-59377600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:59370400-59371000	Enhancers	Small Intestine	intestine
42	chr1:59370400-59371400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:59370400-59371800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:59370400-59371800	Enhancers	Brain Substantia Nigra	brain
45	chr1:59370400-59372400	Enhancers	A549	lung
46	chr1:59370400-59374400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:59370400-59374400	Weak transcription	Adipose Nuclei	Adipose
48	chr1:59370600-59374200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:59370600-59374200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:59370600-59374200	Weak transcription	HMEC	breast

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