Variant report

Variant	rs4848281
Chromosome Location	chr2:112945188-112945189
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112941329..112944537-chr2:112945158..112947736,3	K562	blood:
2	chr2:112944701..112946678-chr2:112951279..112953593,2	K562	blood:
3	chr2:112944016..112946935-chr2:113032135..113034643,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11123130	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11676628	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11691239	0.89[ASN][1000 genomes]
rs11903915	0.89[ASN][1000 genomes]
rs12613586	0.93[AFR][1000 genomes]
rs12711736	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849051	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708607	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6761440	0.89[ASN][1000 genomes]
rs72831633	0.89[ASN][1000 genomes]
rs72831634	0.89[ASN][1000 genomes]
rs72831636	0.89[ASN][1000 genomes]
rs72831638	0.89[ASN][1000 genomes]
rs72831641	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4848281	RGPD8	cis	Esophagus Mucosa	GTEx
rs4848281	RGPD8	cis	lung	GTEx
rs4848281	RGPD8	cis	Adipose Subcutaneous	GTEx
rs4848281	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	chr2:112939600-112946400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:112939600-112946600	Weak transcription	Gastric	stomach
4	chr2:112940400-112946400	Weak transcription	Right Ventricle	heart
5	chr2:112941000-112946000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:112941200-112945200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr2:112942000-112945400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:112942600-112945200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr2:112943200-112952200	Weak transcription	Fetal Lung	lung
10	chr2:112943400-112948200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:112943800-112945200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:112944000-112945200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:112944200-112945800	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:112944400-112945200	Enhancers	Primary T cells from cord blood	blood
15	chr2:112944400-112945200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:112944400-112945400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:112944400-112945400	Genic enhancers	Thymus	Thymus
18	chr2:112944600-112945200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr2:112944600-112945200	ZNF genes & repeats	Fetal Stomach	stomach
20	chr2:112944600-112945200	Genic enhancers	Fetal Thymus	thymus
21	chr2:112944800-112946600	Enhancers	Primary B cells from peripheral blood	blood
22	chr2:112944800-112946600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:112944800-112946800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr2:112944800-112947000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:112945000-112945200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:112945000-112945400	Weak transcription	Spleen	Spleen
27	chr2:112945000-112945600	Enhancers	HUVEC	blood vessel
28	chr2:112945000-112945600	Enhancers	K562	blood
29	chr2:112945000-112946200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:112945000-112946200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr2:112945000-112946200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr2:112945000-112946200	Enhancers	Dnd41	blood

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