Variant report

Variant	rs1360294
Chromosome Location	chr1:170043851-170043852
allele	C/T
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	MAX	chr1:170043411-170044134	MCF-7	breast:	n/a	n/a
2	RAD21	chr1:170043684-170044141	HepG2	liver:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
3	KAP1	chr1:170043352-170044382	HEK293	kidney:	n/a	n/a
4	POLR2A	chr1:170043464-170044102	ECC-1	luminal epithelium:	n/a	n/a
5	SMC3	chr1:170043572-170044545	GM12878	blood:	n/a	n/a
6	TCF12	chr1:170043461-170043887	GM12878	blood:	n/a	chr1:170043733-170043743
7	RAD21	chr1:170043621-170044222	Hela-S3	cervix:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
8	NRF1	chr1:170043301-170044177	SK-N-SH	brain:	n/a	chr1:170043852-170043863 chr1:170043854-170043863 chr1:170043882-170043896 chr1:170043881-170043892
9	CTCF	chr1:170043447-170044359	K562	blood:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
10	TBL1XR1	chr1:170043418-170044306	K562	blood:	n/a	n/a
11	CREB1	chr1:170043444-170044055	A549	lung:	n/a	n/a
12	TEAD4	chr1:170043665-170044122	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:170043228-170044159	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr1:170043396-170044174	K562	blood:	n/a	n/a
15	SIN3AK20	chr1:170043439-170044198	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:170043628-170044153	HUVEC	blood vessel:	n/a	n/a
17	TBL1XR1	chr1:170043535-170044541	K562	blood:	n/a	n/a
18	HEY1	chr1:170043464-170043939	K562	blood:	n/a	chr1:170043733-170043748 chr1:170043731-170043746
19	POLR2A	chr1:170043400-170044007	HepG2	liver:	n/a	n/a
20	ELF1	chr1:170043394-170044037	GM12878	blood:	n/a	chr1:170043609-170043618
21	CCNT2	chr1:170043424-170044211	K562	blood:	n/a	n/a
22	SIN3AK20	chr1:170043286-170043919	H1-hESC	embryonic stem cell:	n/a	n/a
23	PML	chr1:170043500-170044147	K562	blood:	n/a	n/a
24	MXI1	chr1:170043002-170044283	IMR90	lung:	n/a	n/a
25	CTCF	chr1:170043592-170044094	MCF-7	breast:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
26	CREB1	chr1:170043451-170044223	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZBTB7A	chr1:170043536-170043852	K562	blood:	n/a	n/a
28	MXI1	chr1:170043038-170044623	GM12878	blood:	n/a	n/a
29	NRF1	chr1:170043456-170044286	GM12878	blood:	n/a	chr1:170043852-170043863 chr1:170043854-170043863 chr1:170043882-170043896 chr1:170043881-170043892
30	MYBL2	chr1:170043522-170044243	HepG2	liver:	n/a	chr1:170044056-170044069
31	CTCF	chr1:170043826-170044132	Kidney_OC	kidney:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
32	YY1	chr1:170043231-170044027	H1-hESC	embryonic stem cell:	n/a	chr1:170043612-170043626 chr1:170043242-170043252 chr1:170043616-170043627
33	MAX	chr1:170043405-170044188	MCF-7	breast:	n/a	n/a
34	CTCF	chr1:170043556-170044278	K562	blood:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
35	POLR2A	chr1:170042533-170044483	GM12891	blood:	n/a	n/a
36	RCOR1	chr1:170043688-170044082	HepG2	liver:	n/a	n/a
37	RAD21	chr1:170043687-170044295	A549	lung:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
38	RFX5	chr1:170043500-170044265	Hela-S3	cervix:	n/a	n/a
39	RAD21	chr1:170043579-170044197	IMR90	lung:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
40	SP1	chr1:170043463-170044153	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:170043422-170044087	K562	blood:	n/a	n/a
42	MAX	chr1:170043370-170044202	SK-N-SH	brain:	n/a	n/a
43	CHD2	chr1:170043400-170044114	GM12878	blood:	n/a	n/a
44	STAT3	chr1:170043603-170044481	GM12878	blood:	n/a	n/a
45	CTCF	chr1:170043637-170044109	Lung_OC	lung:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
46	CUX1	chr1:170043835-170044977	GM12878	blood:	n/a	chr1:170044699-170044713 chr1:170044698-170044707
47	CTCF	chr1:170043462-170044396	GM12878	blood:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
48	RAD21	chr1:170043833-170044121	K562	blood:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
49	CTCF	chr1:170043433-170044542	A549	lung:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
50	POLR2A	chr1:170043400-170044205	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170042562..170044134-chr1:170053938..170056849,2	K562	blood:
2	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:

Variant related genes	Relation type
KIFAP3	TF binding region
ENSG00000075945	Chromatin interaction
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10800496	0.89[CHB][hapmap]
rs11577641	0.88[CEU][hapmap]
rs11579102	0.88[CEU][hapmap]
rs11579254	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11584208	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11588736	0.88[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1572551	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862870	0.89[EUR][1000 genomes]
rs16862874	0.91[EUR][1000 genomes]
rs16862902	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs16862943	0.96[EUR][1000 genomes]
rs1928887	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2150111	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3753312	0.88[CEU][hapmap]
rs41496844	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4656202	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656730	0.96[EUR][1000 genomes]
rs4656731	0.96[EUR][1000 genomes]
rs4656732	0.88[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56041446	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59916635	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61806098	0.89[EUR][1000 genomes]
rs61825319	0.91[EUR][1000 genomes]
rs61825320	0.93[EUR][1000 genomes]
rs61825343	0.96[EUR][1000 genomes]
rs61825344	0.96[EUR][1000 genomes]
rs61825346	0.95[EUR][1000 genomes]
rs61825347	0.96[EUR][1000 genomes]
rs61825348	0.96[EUR][1000 genomes]
rs61825352	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825353	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825354	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825356	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825358	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61827261	0.85[AMR][1000 genomes]
rs6657215	0.83[CHB][hapmap]
rs73035088	0.94[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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170041000-170044200	Active TSS	GM12878-XiMat	blood
2	chr1:170041400-170044200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:170042000-170044200	Active TSS	HMEC	breast
4	chr1:170042000-170044200	Active TSS	K562	blood
5	chr1:170042000-170044400	Active TSS	NHLF	lung
6	chr1:170042000-170044600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:170042200-170044000	Active TSS	Brain Angular Gyrus	brain
8	chr1:170042400-170044200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:170042400-170044200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:170042400-170044200	Active TSS	Fetal Lung	lung
11	chr1:170042400-170044200	Active TSS	NHDF-Ad	bronchial
12	chr1:170042400-170044600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:170042600-170044200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:170042600-170044200	Active TSS	Brain Germinal Matrix	brain
15	chr1:170042600-170044200	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:170042600-170044400	Active TSS	Aorta	Aorta
17	chr1:170042600-170044400	Active TSS	Brain Substantia Nigra	brain
18	chr1:170042600-170044400	Active TSS	Fetal Brain Male	brain
19	chr1:170042600-170044400	Active TSS	Fetal Brain Female	brain
20	chr1:170042600-170044400	Active TSS	Fetal Intestine Large	intestine
21	chr1:170042600-170044400	Active TSS	Ovary	ovary
22	chr1:170042600-170044400	Active TSS	Psoas Muscle	Psoas
23	chr1:170042600-170044400	Active TSS	Stomach Mucosa	stomach
24	chr1:170042600-170044400	Active TSS	A549	lung
25	chr1:170042600-170044600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:170042600-170044600	Active TSS	Right Ventricle	heart
27	chr1:170042800-170044200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:170042800-170044200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:170042800-170044200	Active TSS	Fetal Stomach	stomach
30	chr1:170042800-170044200	Active TSS	NH-A	brain
31	chr1:170042800-170044400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:170042800-170044400	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr1:170042800-170044400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:170042800-170044400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:170042800-170044400	Active TSS	Brain Anterior Caudate	brain
36	chr1:170042800-170044400	Active TSS	Brain Cingulate Gyrus	brain
37	chr1:170042800-170044600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr1:170042800-170044600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:170042800-170044600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr1:170042800-170044600	Active TSS	Right Atrium	heart
41	chr1:170043000-170044000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:170043000-170044000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:170043000-170044000	Active TSS	Osteobl	bone
44	chr1:170043000-170044200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:170043000-170044200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:170043000-170044200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:170043000-170044200	Active TSS	Brain Hippocampus Middle	brain
48	chr1:170043000-170044200	Active TSS	Colon Smooth Muscle	Colon
49	chr1:170043000-170044200	Active TSS	Esophagus	oesophagus
50	chr1:170043000-170044200	Active TSS	Fetal Intestine Small	intestine

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