Variant report

Variant	rs35000319
Chromosome Location	chr1:84542492-84542493
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:84542478-84542560	K562	blood:	n/a	n/a
2	MXI1	chr1:84541895-84545296	SK-N-SH	brain:	n/a	n/a
3	MYC	chr1:84542463-84543380	MCF10A-Er-Src	breast:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
4	POLR2A	chr1:84542451-84544567	Hela-S3	cervix:	n/a	n/a
5	ZKSCAN1	chr1:84542430-84544041	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:84542201-84544432	MCF10A-Er-Src	breast:	n/a	n/a
7	TBP	chr1:84542458-84543576	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:84463410..84466364-chr1:84542152..84546505,5	K562	blood:
2	chr1:84542242..84543745-chr1:85154770..85157524,2	K562	blood:
3	chr1:84387778..84389882-chr1:84541236..84543359,2	K562	blood:
4	chr1:84540590..84543508-chr1:84558962..84560991,2	K562	blood:
5	chr1:84541598..84548799-chr1:84549003..84554628,15	K562	blood:
6	chr1:84377090..84379247-chr1:84542414..84544902,2	K562	blood:
7	chr1:84540791..84543154-chr1:84633401..84635166,2	K562	blood:
8	chr1:84541371..84543109-chr1:84583953..84586517,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTLL7-3	chr1:84542062-84543325	XLOC_000889
2	lnc-TTLL7-3	chr1:84542014-84543614	ENSG00000271576.1
3	lnc-TTLL7-3	chr1:84542014-84543655	NONHSAT004184

No data

Variant related genes	Relation type
PRKACB	TF binding region
ENSG00000137941	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000213540	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11163870	0.84[ASN][1000 genomes]
rs12094835	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12129674	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12563929	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs12567738	0.98[ASN][1000 genomes]
rs12734711	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1521519	0.93[ASN][1000 genomes]
rs17130873	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs17475438	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34654680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880060	0.98[ASN][1000 genomes]
rs34972329	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35105659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35760860	0.98[ASN][1000 genomes]
rs35960022	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36173422	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41300540	0.91[ASN][1000 genomes]
rs57443421	0.84[ASN][1000 genomes]
rs59779864	0.80[ASN][1000 genomes]
rs60455471	0.88[ASN][1000 genomes]
rs61360062	0.90[ASN][1000 genomes]
rs61766872	0.84[ASN][1000 genomes]
rs6699590	0.88[ASN][1000 genomes]
rs71652665	0.98[ASN][1000 genomes]
rs71652666	0.98[ASN][1000 genomes]
rs71652667	0.98[ASN][1000 genomes]
rs72721436	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3379138	chr1:84531980-84545128	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35000319	C1orf52	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84538400-84542800	Weak transcription	HSMM	muscle
2	chr1:84541400-84542600	Weak transcription	Brain Substantia Nigra	brain
3	chr1:84542000-84542800	Enhancers	Liver	Liver
4	chr1:84542000-84544600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:84542000-84544800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:84542000-84545200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:84542200-84542600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:84542200-84542800	Enhancers	Brain Angular Gyrus	brain
9	chr1:84542200-84542800	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:84542200-84542800	Flanking Active TSS	Hela-S3	cervix
11	chr1:84542200-84543000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:84542400-84542600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:84542400-84542600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:84542400-84542600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:84542400-84542600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:84542400-84542600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:84542400-84542600	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr1:84542400-84542600	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr1:84542400-84542600	Enhancers	Brain Germinal Matrix	brain
20	chr1:84542400-84542600	Enhancers	Colon Smooth Muscle	Colon
21	chr1:84542400-84542600	Active TSS	Fetal Brain Female	brain
22	chr1:84542400-84542600	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr1:84542400-84542600	Enhancers	Fetal Muscle Leg	muscle
24	chr1:84542400-84542600	Flanking Active TSS	A549	lung
25	chr1:84542400-84542600	Enhancers	HUVEC	blood vessel
26	chr1:84542400-84542600	Flanking Active TSS	K562	blood
27	chr1:84542400-84542600	Enhancers	NH-A	brain
28	chr1:84542400-84542600	Enhancers	NHEK	skin
29	chr1:84542400-84542600	Enhancers	NHLF	lung
30	chr1:84542400-84542600	Enhancers	Osteobl	bone
31	chr1:84542400-84542800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:84542400-84542800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:84542400-84542800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:84542400-84542800	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:84542400-84542800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:84542400-84542800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:84542400-84542800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:84542400-84542800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:84542400-84542800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:84542400-84542800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:84542400-84542800	Enhancers	Fetal Intestine Large	intestine
42	chr1:84542400-84542800	Enhancers	Fetal Intestine Small	intestine
43	chr1:84542400-84542800	Enhancers	Fetal Stomach	stomach
44	chr1:84542400-84542800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:84542400-84542800	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr1:84542400-84542800	Flanking Active TSS	HepG2	liver
47	chr1:84542400-84542800	Flanking Active TSS	HSMMtube	muscle
48	chr1:84542400-84542800	Flanking Active TSS	NHDF-Ad	bronchial
49	chr1:84542400-84543000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:84542400-84543000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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