Variant report

Variant	rs259684
Chromosome Location	chr6:37896317-37896318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL353597.1-11	chr6:37896219-37896620	expReg_chr6_4564_+

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10456096	0.82[EUR][1000 genomes]
rs10456097	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10807188	0.82[EUR][1000 genomes]
rs1187422	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1187423	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12192182	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12198907	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12200258	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12206818	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211248	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211981	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12213835	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13210701	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13214465	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13220131	0.84[EUR][1000 genomes]
rs171831	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1812599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2132597	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2395686	0.82[EUR][1000 genomes]
rs259673	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259686	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259689	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259690	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259691	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259695	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259713	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259715	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259716	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2645102	0.80[EUR][1000 genomes]
rs2645107	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2645113	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2645116	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2645120	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2645127	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2645128	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2645131	0.80[EUR][1000 genomes]
rs2645134	0.81[EUR][1000 genomes]
rs2645137	0.81[EUR][1000 genomes]
rs2842500	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2842517	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842527	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2842529	0.84[EUR][1000 genomes]
rs34871463	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35823566	0.81[ASN][1000 genomes]
rs56098839	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458027	0.83[EUR][1000 genomes]
rs6458028	0.82[EUR][1000 genomes]
rs7755089	0.81[EUR][1000 genomes]
rs9296232	0.82[EUR][1000 genomes]
rs9394460	0.82[EUR][1000 genomes]
rs9647619	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966705	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:37874600-37903800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:37876600-37903200	Weak transcription	Dnd41	blood
5	chr6:37878800-37900400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:37880000-37896600	Weak transcription	Right Ventricle	heart
7	chr6:37880000-37898000	Weak transcription	Fetal Thymus	thymus
8	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
9	chr6:37884600-37904800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:37884800-37898200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:37884800-37917000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:37885200-37906200	Weak transcription	HSMM	muscle
13	chr6:37885600-37896800	Weak transcription	Fetal Brain Male	brain
14	chr6:37886400-37896400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:37886600-37896600	Weak transcription	Fetal Intestine Small	intestine
16	chr6:37887600-37933200	Weak transcription	NHDF-Ad	bronchial
17	chr6:37887800-37896400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:37887800-37906200	Weak transcription	HSMMtube	muscle
19	chr6:37887800-37906600	Weak transcription	NH-A	brain
20	chr6:37888600-37903600	Weak transcription	Osteobl	bone
21	chr6:37888800-37898000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:37888800-37898600	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:37888800-37903800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:37889000-37896400	Weak transcription	Brain Anterior Caudate	brain
25	chr6:37889000-37897000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:37889000-37897000	Weak transcription	A549	lung
27	chr6:37889000-37898000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:37889000-37898200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:37889000-37906400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:37889200-37898000	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:37889200-37898200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:37889200-37898600	Weak transcription	Brain Substantia Nigra	brain
33	chr6:37889200-37903600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:37889800-37903800	Weak transcription	Aorta	Aorta
35	chr6:37890800-37910400	Weak transcription	NHEK	skin
36	chr6:37891000-37900800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:37891200-37896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:37892400-37902800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:37892400-37903400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:37892400-37904000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:37892400-37904400	Weak transcription	GM12878-XiMat	blood
42	chr6:37892400-37907200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:37892600-37896400	Weak transcription	Spleen	Spleen
44	chr6:37892600-37896600	Weak transcription	Stomach Mucosa	stomach
45	chr6:37892600-37903800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:37892600-37905000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:37892600-37910800	Weak transcription	Primary B cells from cord blood	blood
48	chr6:37892600-37928800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:37892800-37898000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:37892800-37903400	Weak transcription	Primary T cells from cord blood	blood

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