Variant report

Variant	rs1556260
Chromosome Location	chr1:161014446-161014447
allele	A/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	CHD2	chr1:161014386-161015097	GM12878	blood:	n/a	n/a
3	NRF1	chr1:161014437-161016739	SK-N-SH	brain:	n/a	chr1:161015725-161015736 chr1:161015334-161015343
4	POLR2A	chr1:161014375-161017763	GM12878	blood:	n/a	n/a
5	MTA3	chr1:161014325-161017601	GM12878	blood:	n/a	n/a
6	MAX	chr1:161014407-161015203	GM12878	blood:	n/a	n/a
7	EP300	chr1:161014174-161015033	GM12878	blood:	n/a	chr1:161014768-161014782 chr1:161014218-161014227 chr1:161014774-161014788 chr1:161014885-161014894
8	SPI1	chr1:161014364-161015210	GM12878	blood:	n/a	chr1:161014773-161014782 chr1:161014828-161014841 chr1:161014830-161014839 chr1:161014827-161014840
9	MXI1	chr1:161014011-161016561	SK-N-SH	brain:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
10	TBL1XR1	chr1:161014437-161015331	GM12878	blood:	n/a	n/a
11	HCFC1	chr1:161014027-161016818	Hela-S3	cervix:	n/a	n/a
12	BCLAF1	chr1:161014435-161015273	GM12878	blood:	n/a	chr1:161014779-161014788 chr1:161014773-161014782
13	SIN3A	chr1:161014282-161016801	GM12878	blood:	n/a	chr1:161015720-161015728 chr1:161015266-161015277
14	ATF2	chr1:161014435-161014999	GM12878	blood:	n/a	n/a
15	TAF1	chr1:161014354-161016385	H1-neurons	neurons:	n/a	n/a
16	STAT5A	chr1:161014375-161017198	GM12878	blood:	n/a	chr1:161014773-161014784 chr1:161015988-161015997 chr1:161015462-161015474 chr1:161015361-161015369 chr1:161014779-161014790 chr1:161015987-161015996
17	IRF1	chr1:161014446-161016216	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
18	WRNIP1	chr1:161014440-161015165	GM12878	blood:	n/a	n/a
19	MXI1	chr1:161014003-161015822	IMR90	lung:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
20	RELA	chr1:161014438-161015255	GM19099	blood:	n/a	n/a
21	REST	chr1:161013920-161016847	H1-neurons	neurons:	n/a	chr1:161015428-161015437
22	MYC	chr1:161014411-161016221	K562	blood:	n/a	n/a
23	POLR2A	chr1:161014337-161016449	H1-neurons	neurons:	n/a	n/a
24	CHD1	chr1:161014386-161016735	GM12878	blood:	n/a	n/a
25	MXI1	chr1:161014275-161015131	K562	blood:	n/a	chr1:161014433-161014448 chr1:161014431-161014446
26	ZNF384	chr1:161014334-161014873	GM12878	blood:	n/a	n/a
27	PML	chr1:161014226-161017644	GM12878	blood:	n/a	n/a
28	NFIC	chr1:161014414-161015067	GM12878	blood:	n/a	n/a
29	ZNF384	chr1:161014385-161014639	K562	blood:	n/a	n/a
30	NFIC	chr1:161014145-161015167	GM12878	blood:	n/a	n/a
31	CEBPB	chr1:161014435-161015147	GM12878	blood:	n/a	n/a
32	CTCF	chr1:161014440-161014590	BJ	skin:	n/a	n/a
33	POLR2A	chr1:161014368-161016407	H1-neurons	neurons:	n/a	n/a
34	CTCF	chr1:161014420-161014570	HCPEpiC	choroid plexus:	n/a	n/a
35	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
ENSG00000140939	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000186517	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12036299	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1556259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832617	0.87[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs1974140	0.92[EUR][1000 genomes]
rs2073653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766382	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766383	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4617422	1.00[CEU][hapmap]
rs57839241	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58318788	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs58974723	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6427572	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427573	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660240	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6686076	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695707	0.87[TSI][hapmap]
rs6701822	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7516231	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1556260	ITLN1	cis	cerebellum	SCAN
rs1556260	F11R	cis	cerebellum	SCAN
rs1556260	SDHC	cis	parietal	SCAN
rs1556260	ARHGEF11	cis	cerebellum	SCAN
rs1556260	TSTD1	cis	Lymphoblastoid	GTEx
rs1556260	TSTD1	cis	lymphoblastoid	seeQTL
rs1556260	ASH1L	cis	cerebellum	SCAN
rs1556260	FCGR2A	cis	parietal	SCAN
rs1556260	OR10K1	cis	cerebellum	SCAN
rs1556260	KCNJ9	cis	cerebellum	SCAN
rs1556260	SNORA42	cis	cerebellum	SCAN
rs1556260	KIRREL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161012000-161014600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:161013200-161014600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:161013200-161014600	Weak transcription	Gastric	stomach
4	chr1:161013400-161014600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:161013800-161014600	Enhancers	Spleen	Spleen
6	chr1:161014000-161014600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:161014000-161014600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr1:161014000-161014600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:161014000-161014600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr1:161014000-161014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:161014000-161014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:161014000-161014600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:161014000-161014600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:161014000-161014600	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr1:161014000-161014600	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr1:161014000-161014600	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr1:161014000-161014600	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:161014000-161014600	Flanking Active TSS	Fetal Thymus	thymus
19	chr1:161014000-161014600	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr1:161014000-161014600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr1:161014000-161014600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:161014000-161014600	Flanking Active TSS	NHEK	skin
23	chr1:161014000-161014800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:161014000-161014800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr1:161014000-161014800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:161014000-161014800	Flanking Active TSS	Fetal Brain Male	brain
27	chr1:161014000-161014800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:161014000-161014800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:161014000-161014800	Flanking Active TSS	HSMMtube	muscle
30	chr1:161014000-161014800	Flanking Active TSS	HUVEC	blood vessel
31	chr1:161014000-161014800	Flanking Active TSS	K562	blood
32	chr1:161014000-161014800	Flanking Active TSS	NH-A	brain
33	chr1:161014000-161015000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr1:161014000-161015200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr1:161014000-161015400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:161014000-161016200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:161014000-161016400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:161014000-161016400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:161014000-161017200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:161014200-161014600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:161014200-161014600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:161014200-161014600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:161014200-161014600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:161014200-161014600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:161014200-161014600	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr1:161014200-161014600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr1:161014200-161014600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:161014200-161014600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:161014200-161014600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr1:161014200-161014600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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