Variant report

Variant	rs6832655
Chromosome Location	chr4:8359839-8359840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HTRA3-4	chr4:8358805-8360149	NONHSAT095089
2	lnc-ACOX3-1	chr4:8356817-8360065	ENSG00000251615.3

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10018660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12507368	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12508944	1.00[ASN][1000 genomes]
rs13102851	1.00[ASN][1000 genomes]
rs13103277	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129831	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2280570	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28690830	0.84[ASN][1000 genomes]
rs34893440	1.00[ASN][1000 genomes]
rs36074936	1.00[ASN][1000 genomes]
rs57254469	1.00[ASN][1000 genomes]
rs6824623	1.00[ASN][1000 genomes]
rs7657076	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv470013	chr4:8315938-8377058	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv878605	chr4:8332057-8378959	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878606	chr4:8349738-8377058	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878607	chr4:8349738-8380857	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv878608	chr4:8349738-8386720	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv461219	chr4:8353829-8390646	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv593637	chr4:8353829-8390646	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	nsv526508	chr4:8357923-8371554	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv966468	chr4:8358228-8374418	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6832655	IP6K1	trans	parietal	SCAN
rs6832655	ABLIM2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8351600-8362800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr4:8353400-8366200	Weak transcription	Aorta	Aorta
3	chr4:8353600-8366000	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:8354200-8360000	Weak transcription	Brain Anterior Caudate	brain
5	chr4:8354200-8366200	Weak transcription	Brain Substantia Nigra	brain
6	chr4:8354400-8366000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:8354400-8366000	Weak transcription	Brain Angular Gyrus	brain
8	chr4:8354400-8367000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:8354400-8367200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:8354600-8381000	Weak transcription	Right Atrium	heart
11	chr4:8355000-8366200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:8355400-8365400	Weak transcription	Left Ventricle	heart
13	chr4:8355400-8366000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:8355800-8366000	Weak transcription	Lung	lung
15	chr4:8355800-8366200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:8355800-8384800	Weak transcription	Fetal Lung	lung
17	chr4:8356200-8366200	Weak transcription	Thymus	Thymus
18	chr4:8356400-8360200	Enhancers	HMEC	breast
19	chr4:8356600-8360400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:8356800-8360000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:8356800-8360400	Enhancers	NHEK	skin
22	chr4:8357000-8360400	Enhancers	Fetal Stomach	stomach
23	chr4:8357600-8360200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:8357600-8360200	Enhancers	Ovary	ovary
25	chr4:8357600-8360600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:8357800-8361600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:8358200-8360400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:8358400-8366000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:8358400-8366200	Weak transcription	HSMM	muscle
30	chr4:8358400-8366200	Weak transcription	HSMMtube	muscle
31	chr4:8358400-8366800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:8358600-8362400	Weak transcription	Fetal Heart	heart
33	chr4:8358600-8365800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:8358600-8368200	Weak transcription	Fetal Kidney	kidney
35	chr4:8358800-8361200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:8358800-8361200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:8358800-8366000	Weak transcription	Esophagus	oesophagus
38	chr4:8359000-8360200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:8359000-8367200	Weak transcription	Gastric	stomach
40	chr4:8359200-8360200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr4:8359200-8366800	Weak transcription	Brain Germinal Matrix	brain
42	chr4:8359400-8360000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr4:8359400-8360000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:8359400-8360000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
45	chr4:8359400-8360200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr4:8359400-8360200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr4:8359400-8360400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:8359400-8360600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr4:8359600-8360000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr4:8359600-8360200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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