Variant report

Variant	rs3811643
Chromosome Location	chr2:112940578-112940579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12711735	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13387246	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13394408	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13402356	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848280	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849050	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7557904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7591933	0.88[EUR][1000 genomes];0.94[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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3811643	ZC3H8	cis	parietal	SCAN
rs3811643	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112939000-112940600	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr2:112939000-112940600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr2:112939000-112941200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:112939000-112941600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr2:112939200-112940600	Flanking Active TSS	Fetal Thymus	thymus
7	chr2:112939200-112941600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:112939200-112942800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:112939400-112941200	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr2:112939400-112941200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr2:112939400-112942000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:112939400-112944400	Weak transcription	Spleen	Spleen
13	chr2:112939600-112940800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:112939600-112941400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr2:112939600-112941800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:112939600-112944400	Weak transcription	Pancreas	Pancrea
17	chr2:112939600-112946400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:112939600-112946600	Weak transcription	Gastric	stomach
19	chr2:112939800-112940600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr2:112939800-112940600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:112939800-112940600	Enhancers	HSMMtube	muscle
22	chr2:112939800-112941000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:112939800-112941000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:112939800-112941600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr2:112939800-112944800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:112940000-112941800	Enhancers	Dnd41	blood
27	chr2:112940200-112940600	Flanking Active TSS	Thymus	Thymus
28	chr2:112940400-112940600	Enhancers	Fetal Muscle Leg	muscle
29	chr2:112940400-112940800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:112940400-112940800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:112940400-112941000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:112940400-112946400	Weak transcription	Right Ventricle	heart

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