Variant report

Variant	rs59916635
Chromosome Location	chr1:170042694-170042695
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	POLR2A	chr1:170042570-170043112	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:170042535-170042961	GM12892	blood:	n/a	n/a
3	TAF7	chr1:170042517-170042922	K562	blood:	n/a	n/a
4	POLR2A	chr1:170042533-170044483	GM12891	blood:	n/a	n/a
5	TAF7	chr1:170042640-170042797	K562	blood:	n/a	n/a
6	POLR2A	chr1:170042503-170043212	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:170042508-170044157	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:170042592-170042940	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:170042539-170044633	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:170042574-170042949	GM12891	blood:	n/a	n/a
11	MYC	chr1:170042623-170042823	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:170042544-170042856	K562	blood:	n/a	n/a
13	POLR2A	chr1:170042564-170042949	K562	blood:	n/a	n/a
14	POLR2A	chr1:170042163-170044116	MCF10A-Er-Src	breast:	n/a	n/a
15	MXI1	chr1:170042598-170044745	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:170042536-170042976	GM12891	blood:	n/a	n/a
17	RAD21	chr1:170042638-170044409	SK-N-SH	brain:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
18	POLR2A	chr1:170042620-170042868	Hela-S3	cervix:	n/a	n/a
19	TBP	chr1:170042430-170044552	GM12878	blood:	n/a	n/a
20	EBF1	chr1:170042606-170044754	GM12878	blood:	n/a	n/a
21	REST	chr1:170042381-170044192	H1-neurons	neurons:	n/a	chr1:170043622-170043635 chr1:170043552-170043561 chr1:170043774-170043787
22	POLR2A	chr1:170042576-170044168	GM18505	blood:	n/a	n/a
23	TBP	chr1:170042548-170042826	K562	blood:	n/a	n/a
24	POLR2A	chr1:170042473-170044175	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr1:170042528-170042900	GM12891	blood:	n/a	n/a
26	HEY1	chr1:170042583-170042942	K562	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	chr1:170037046..170038634-chr1:170041259..170042880,2	K562	blood:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11579254	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11584208	0.92[EUR][1000 genomes]
rs11588736	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1360294	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1572551	0.85[EUR][1000 genomes]
rs16862870	0.92[EUR][1000 genomes]
rs16862874	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs16862902	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16862943	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1928887	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2150111	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41496844	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4656202	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4656730	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4656731	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4656732	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56041446	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806098	0.92[EUR][1000 genomes]
rs61825319	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61825320	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825343	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61825344	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825346	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825347	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825348	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61825352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61825353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61825354	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61825356	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827261	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73035088	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73041144	0.81[AFR][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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:170036600-170043000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:170037000-170042800	Weak transcription	Right Atrium	heart
4	chr1:170037000-170043000	Weak transcription	Left Ventricle	heart
5	chr1:170037000-170043200	Weak transcription	Small Intestine	intestine
6	chr1:170037200-170043200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:170037400-170043000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:170038000-170043200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:170038600-170043000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:170038600-170043000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:170040000-170043000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:170041000-170043000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:170041000-170043200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:170041000-170044200	Active TSS	GM12878-XiMat	blood
15	chr1:170041200-170043000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:170041400-170043000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:170041400-170043400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:170041400-170044200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:170042000-170043000	Enhancers	Colon Smooth Muscle	Colon
20	chr1:170042000-170043200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:170042000-170044200	Active TSS	HMEC	breast
22	chr1:170042000-170044200	Active TSS	K562	blood
23	chr1:170042000-170044400	Active TSS	NHLF	lung
24	chr1:170042000-170044600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:170042200-170042800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:170042200-170042800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:170042200-170043400	Flanking Active TSS	Dnd41	blood
28	chr1:170042200-170044000	Active TSS	Brain Angular Gyrus	brain
29	chr1:170042400-170042800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:170042400-170042800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:170042400-170043000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:170042400-170043000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr1:170042400-170043000	Enhancers	Hela-S3	cervix
34	chr1:170042400-170043200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:170042400-170044200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:170042400-170044200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:170042400-170044200	Active TSS	Fetal Lung	lung
38	chr1:170042400-170044200	Active TSS	NHDF-Ad	bronchial
39	chr1:170042400-170044600	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:170042600-170042800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:170042600-170042800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:170042600-170042800	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr1:170042600-170042800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:170042600-170042800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:170042600-170042800	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr1:170042600-170042800	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr1:170042600-170042800	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr1:170042600-170042800	Flanking Active TSS	Fetal Stomach	stomach
49	chr1:170042600-170042800	Active TSS	Rectal Smooth Muscle	rectum
50	chr1:170042600-170042800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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