Variant report

Variant	rs904323
Chromosome Location	chr1:222790366-222790367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:222790053-222791684	IMR90	lung:	n/a	n/a
2	MXI1	chr1:222789848-222793177	SK-N-SH	brain:	n/a	chr1:222791038-222791053 chr1:222791036-222791051
3	RCOR1	chr1:222789522-222791271	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:222761567..222764879-chr1:222790132..222793494,4	MCF-7	breast:
2	chr1:222790149..222792584-chr1:222885363..222887404,2	K562	blood:
3	chr1:222788058..222793799-chr1:222815102..222819462,10	K562	blood:
4	chr1:222789930..222793106-chr1:222884660..222888170,6	K562	blood:
5	chr1:222788934..222792471-chr1:222815936..222819007,5	MCF-7	breast:
6	chr1:222761959..222766700-chr1:222790061..222794365,7	MCF-7	breast:
7	chr1:222789107..222793717-chr1:222814287..222819011,10	K562	blood:

No data

Variant related genes	Relation type
MIA3	TF binding region
ENSG00000154305	Chromatin interaction
ENSG00000229399	Chromatin interaction
ENSG00000143498	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000225265	Chromatin interaction
ENSG00000162819	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17531007	1.00[CHB][hapmap]
rs17531580	1.00[CHB][hapmap]
rs17532757	1.00[ASN][1000 genomes]
rs2378605	1.00[CHB][hapmap]
rs3002141	0.82[EUR][1000 genomes]
rs3002145	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3008621	1.00[ASN][1000 genomes]
rs3008630	1.00[ASN][1000 genomes]
rs4240934	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4256814	1.00[ASN][1000 genomes]
rs61824333	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv3325041	chr1:222790354-222793202	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs904323	PLLP	trans	cerebellum	SCAN
rs904323	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222786400-222790600	Weak transcription	Psoas Muscle	Psoas
2	chr1:222787200-222790600	Weak transcription	K562	blood
3	chr1:222787400-222790600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:222787600-222790600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:222789000-222790600	Enhancers	Colonic Mucosa	Colon
6	chr1:222789200-222790400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:222789600-222790400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:222789600-222790600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:222789800-222790400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:222789800-222790600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:222789800-222790600	Enhancers	HepG2	liver
12	chr1:222789800-222790600	Enhancers	HSMM	muscle
13	chr1:222790000-222790400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:222790000-222790400	Enhancers	Brain Anterior Caudate	brain
15	chr1:222790000-222790400	Enhancers	Osteobl	bone
16	chr1:222790000-222790600	Enhancers	Stomach Mucosa	stomach
17	chr1:222790200-222790400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:222790200-222790400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:222790200-222790400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:222790200-222790400	Enhancers	Adipose Nuclei	Adipose
21	chr1:222790200-222790400	Enhancers	Brain Angular Gyrus	brain
22	chr1:222790200-222790400	Enhancers	Brain Hippocampus Middle	brain
23	chr1:222790200-222790400	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr1:222790200-222790400	Enhancers	Dnd41	blood
25	chr1:222790200-222790600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr1:222790200-222790600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr1:222790200-222790600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:222790200-222790600	Enhancers	Colon Smooth Muscle	Colon
29	chr1:222790200-222790600	Enhancers	Fetal Intestine Large	intestine
30	chr1:222790200-222790600	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr1:222790200-222790600	Enhancers	Fetal Stomach	stomach
32	chr1:222790200-222790600	Bivalent Enhancer	A549	lung
33	chr1:222790200-222790600	Enhancers	NHLF	lung
34	chr1:222790200-222791000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:222790200-222791000	Flanking Active TSS	NHDF-Ad	bronchial
36	chr1:222790200-222791200	Flanking Active TSS	Liver	Liver

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