Variant report

Variant	rs4849057
Chromosome Location	chr2:113010568-113010569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113008666..113014085-chr2:113030385..113035561,7	MCF-7	breast:
2	chr2:112995119..113002036-chr2:113006971..113012595,10	K562	blood:
3	chr2:112640166..112643875-chr2:113008551..113014158,5	K562	blood:
4	chr2:113010163..113016150-chr2:113027955..113035093,25	K562	blood:
5	chr2:113002216..113004918-chr2:113009956..113011920,4	K562	blood:
6	chr2:113009678..113014339-chr2:113236822..113240822,5	K562	blood:
7	chr2:113003810..113005815-chr2:113009554..113011676,2	MCF-7	breast:
8	chr2:113009256..113015419-chr2:113031181..113035814,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000144161	Chromatin interaction
ENSG00000238951	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10169159	0.92[ASN][1000 genomes]
rs10175234	0.84[ASN][1000 genomes]
rs10177573	0.88[ASN][1000 genomes]
rs10183121	0.88[ASN][1000 genomes]
rs10196933	0.81[AMR][1000 genomes]
rs10205038	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123132	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11674953	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11688418	0.93[ASN][1000 genomes]
rs11689487	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11691431	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691794	0.93[ASN][1000 genomes]
rs12620553	0.81[AMR][1000 genomes]
rs12711737	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12711738	0.92[ASN][1000 genomes]
rs34623958	0.92[ASN][1000 genomes]
rs4392265	0.88[ASN][1000 genomes]
rs4446076	0.88[ASN][1000 genomes]
rs4849056	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542045	0.98[ASN][1000 genomes]
rs6542048	0.87[ASN][1000 genomes]
rs6542050	0.88[ASN][1000 genomes]
rs6706874	0.92[ASN][1000 genomes]
rs6716010	0.86[ASN][1000 genomes]
rs6745942	0.88[ASN][1000 genomes]
rs72831684	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7557281	0.86[ASN][1000 genomes]
rs7571435	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601888	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4849057	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
2	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
3	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
5	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
6	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
10	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:112980000-113011800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:112980200-113011600	Weak transcription	HSMM	muscle
13	chr2:112987200-113010800	Weak transcription	NH-A	brain
14	chr2:112987200-113011000	Weak transcription	NHDF-Ad	bronchial
15	chr2:112987400-113011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:112987800-113011000	Weak transcription	NHEK	skin
17	chr2:112987800-113011800	Weak transcription	NHLF	lung
18	chr2:112988400-113011600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:112992200-113011400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:112992200-113011800	Weak transcription	HSMMtube	muscle
21	chr2:112993000-113011000	Weak transcription	HMEC	breast
22	chr2:112993400-113011000	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:112994600-113011800	Weak transcription	Colonic Mucosa	Colon
24	chr2:113001200-113011400	Weak transcription	HUVEC	blood vessel
25	chr2:113004200-113011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:113004400-113011400	Weak transcription	Fetal Heart	heart
27	chr2:113004400-113011600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:113004400-113011800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:113004400-113012000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:113004600-113011400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:113005200-113011400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:113005600-113011000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:113005600-113011400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:113005600-113011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:113005600-113011400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:113005600-113011400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:113005600-113011600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:113005800-113011000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:113005800-113011400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:113005800-113011800	Weak transcription	Aorta	Aorta
41	chr2:113005800-113011800	Weak transcription	Left Ventricle	heart
42	chr2:113005800-113012000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:113006600-113011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:113006800-113011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:113006800-113011400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:113006800-113011800	Weak transcription	Placenta	Placenta
47	chr2:113007000-113010600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:113007000-113011000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:113007000-113011000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:113007000-113011000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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