Variant report

Variant	rs3828021
Chromosome Location	chr1:211306169-211306170
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RD3-2	chr1:211305930-211306368	ENSG00000234233.1

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10494931	0.84[JPT][hapmap]
rs10494932	0.84[JPT][hapmap]
rs10863877	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119658	0.84[JPT][hapmap]
rs11119664	0.84[JPT][hapmap]
rs11119694	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119696	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11579711	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582507	0.84[JPT][hapmap]
rs11583101	0.84[JPT][hapmap]
rs12406301	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408290	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12756697	0.87[JPT][hapmap]
rs12760791	0.84[JPT][hapmap]
rs1338353	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1393028	0.84[JPT][hapmap]
rs1501558	0.84[JPT][hapmap]
rs1501560	0.84[JPT][hapmap]
rs1538287	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572646	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1582137	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17017226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17188797	0.84[JPT][hapmap]
rs17188895	0.93[ASN][1000 genomes]
rs1933524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2211039	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2221250	0.84[JPT][hapmap]
rs28826269	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111218	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111220	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111221	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111226	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120775	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120776	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120777	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125852	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33985151	0.84[JPT][hapmap]
rs3811396	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61848604	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61848648	0.84[ASN][1000 genomes]
rs6540658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540659	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540666	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540667	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540669	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6669706	0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6684075	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697578	0.81[JPT][hapmap]
rs6700303	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516636	0.93[ASN][1000 genomes]
rs7530182	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537388	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs867849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430056	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9430057	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430058	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946142	0.82[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3828021	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211302600-211307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:211303800-211307800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:211304000-211307600	Active TSS	Brain Angular Gyrus	brain
4	chr1:211304200-211306200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:211305200-211307600	Active TSS	Brain Anterior Caudate	brain
6	chr1:211305200-211307800	Active TSS	HSMMtube	muscle
7	chr1:211305400-211307800	Active TSS	HSMM	muscle
8	chr1:211305800-211306200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:211306000-211306200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:211306000-211306200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr1:211306000-211306200	Bivalent/Poised TSS	Osteobl	bone
12	chr1:211306000-211306400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
13	chr1:211306000-211306400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:211306000-211306400	Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:211306000-211306400	Bivalent Enhancer	Fetal Brain Male	brain
16	chr1:211306000-211306400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
17	chr1:211306000-211306600	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr1:211306000-211306600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr1:211306000-211306600	Flanking Active TSS	A549	lung
20	chr1:211306000-211306800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:211306000-211306800	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr1:211306000-211307200	Bivalent/Poised TSS	Colonic Mucosa	Colon
23	chr1:211306000-211307400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:211306000-211307600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr1:211306000-211308000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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