Variant report

Variant	rs2516838
Chromosome Location	chr1:161014370-161014371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:161014360-161016259	K562	blood:	n/a	chr1:161014773-161014787 chr1:161014776-161014790 chr1:161014770-161014784 chr1:161014779-161014793 chr1:161014777-161014790 chr1:161014775-161014789 chr1:161014779-161014789 chr1:161014773-161014794 chr1:161015569-161015582 chr1:161014771-161014791 chr1:161014765-161014785 chr1:161015780-161015794 chr1:161014777-161014790 chr1:161015568-161015588 chr1:161014769-161014783 chr1:161014772-161014781 chr1:161014774-161014785 chr1:161014777-161014790 chr1:161014777-161014791 chr1:161014779-161014790 chr1:161014778-161014795 chr1:161014780-161014791 chr1:161014773-161014783
2	MTA3	chr1:161014325-161017601	GM12878	blood:	n/a	n/a
3	EP300	chr1:161014174-161015033	GM12878	blood:	n/a	chr1:161014768-161014782 chr1:161014218-161014227 chr1:161014774-161014788 chr1:161014885-161014894
4	SPI1	chr1:161014364-161015210	GM12878	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
5	MXI1	chr1:161014011-161016561	SK-N-SH	brain:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
6	HCFC1	chr1:161014027-161016818	Hela-S3	cervix:	n/a	n/a
7	SIN3A	chr1:161014282-161016801	GM12878	blood:	n/a	chr1:161015720-161015728 chr1:161015266-161015277
8	TAF1	chr1:161014354-161016385	H1-neurons	neurons:	n/a	n/a
9	MXI1	chr1:161014003-161015822	IMR90	lung:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
10	REST	chr1:161013920-161016847	H1-neurons	neurons:	n/a	chr1:161015428-161015437
11	POLR2A	chr1:161014337-161016449	H1-neurons	neurons:	n/a	n/a
12	MXI1	chr1:161014275-161015131	K562	blood:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
13	ZNF384	chr1:161014334-161014873	GM12878	blood:	n/a	n/a
14	PML	chr1:161014226-161017644	GM12878	blood:	n/a	n/a
15	NFIC	chr1:161014145-161015167	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:161014368-161016407	H1-neurons	neurons:	n/a	n/a
17	MXI1	chr1:161014288-161016818	GM12878	blood:	n/a	chr1:161016608-161016623 chr1:161016606-161016621 chr1:161014433-161014448 chr1:161014431-161014446

No.	Distal block	Cell Line	Cell type
1	chr1:161013722..161017299-chr1:161066199..161071039,5	MCF-7	breast:
2	chr1:161013470..161017562-chr1:161084888..161088962,4	MCF-7	breast:
3	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
4	chr1:161013542..161018278-chr1:161100825..161104206,7	MCF-7	breast:
5	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
6	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
7	chr1:161014200..161017793-chr1:161057956..161063190,6	MCF-7	breast:
8	chr1:161014274..161014774-chr16:67205347..67205849,2	Hela-S3	cervix:
9	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
10	chr1:161013674..161020196-chr1:161084642..161090709,10	MCF-7	breast:
11	chr1:161011663..161014033-chr1:161014079..161015803,2	K562	blood:
12	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
13	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:
14	chr1:161013921..161016040-chr1:161036662..161039623,2	MCF-7	breast:

Variant related genes	Relation type
USF1	TF binding region
ENSG00000143217	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000140939	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000186517	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000162755	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11265544	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12116949	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs12130871	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2774279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34339899	0.85[ASN][1000 genomes]
rs35925761	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3892375	0.82[JPT][hapmap]
rs4656974	0.92[ASN][1000 genomes]
rs4656977	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2516838	ITLN1	cis	cerebellum	SCAN
rs2516838	OR10K1	cis	cerebellum	SCAN
rs2516838	USF1	cis	lymphoblastoid	seeQTL
rs2516838	KIRREL	cis	parietal	SCAN
rs2516838	F11R	cis	cerebellum	SCAN
rs2516838	PEAR1	cis	cerebellum	SCAN
rs2516838	SNORA42	cis	cerebellum	SCAN
rs2516838	ARHGEF11	cis	cerebellum	SCAN
rs2516838	USF1	cis	multi-tissue	Pritchard
rs2516838	FCGR2A	cis	parietal	SCAN
rs2516838	FCRL1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161010600-161014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:161012000-161014600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:161012600-161014400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:161012600-161014400	Weak transcription	Ovary	ovary
5	chr1:161012800-161014400	Weak transcription	Aorta	Aorta
6	chr1:161012800-161014400	Weak transcription	Esophagus	oesophagus
7	chr1:161013200-161014400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:161013200-161014600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:161013200-161014600	Weak transcription	Gastric	stomach
10	chr1:161013400-161014600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:161013800-161014400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:161013800-161014400	Flanking Active TSS	Dnd41	blood
13	chr1:161013800-161014600	Enhancers	Spleen	Spleen
14	chr1:161014000-161014400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:161014000-161014400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:161014000-161014400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:161014000-161014400	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:161014000-161014400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:161014000-161014400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:161014000-161014400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:161014000-161014400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr1:161014000-161014400	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr1:161014000-161014400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:161014000-161014400	Flanking Active TSS	Small Intestine	intestine
25	chr1:161014000-161014400	Flanking Active TSS	NHDF-Ad	bronchial
26	chr1:161014000-161014400	Flanking Active TSS	NHLF	lung
27	chr1:161014000-161014600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:161014000-161014600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr1:161014000-161014600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr1:161014000-161014600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr1:161014000-161014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:161014000-161014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:161014000-161014600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:161014000-161014600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:161014000-161014600	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr1:161014000-161014600	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr1:161014000-161014600	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr1:161014000-161014600	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:161014000-161014600	Flanking Active TSS	Fetal Thymus	thymus
40	chr1:161014000-161014600	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr1:161014000-161014600	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr1:161014000-161014600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:161014000-161014600	Flanking Active TSS	NHEK	skin
44	chr1:161014000-161014800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:161014000-161014800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr1:161014000-161014800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:161014000-161014800	Flanking Active TSS	Fetal Brain Male	brain
48	chr1:161014000-161014800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr1:161014000-161014800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr1:161014000-161014800	Flanking Active TSS	HSMMtube	muscle

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