Variant report

Variant	rs17311740
Chromosome Location	chr1:61720648-61720649
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	chr1:61719029-61720900	MCF10A-Er-Src	breast:	n/a	n/a
2	USF1	chr1:61720357-61720769	SK-N-SH_RA	brain:	n/a	chr1:61720624-61720640
3	MYC	chr1:61720394-61720960	MCF10A-Er-Src	breast:	n/a	n/a
4	USF1	chr1:61720398-61720777	K562	blood:	n/a	chr1:61720624-61720640
5	MYC	chr1:61720441-61720704	MCF10A-Er-Src	breast:	n/a	n/a
6	USF1	chr1:61720509-61720717	SK-N-SH_RA	brain:	n/a	chr1:61720624-61720640
7	POLR2A	chr1:61720416-61721117	SK-N-MC	brain:	n/a	n/a
8	MAX	chr1:61719933-61721384	NB4	blood:	n/a	chr1:61721213-61721223 chr1:61721173-61721183
9	POLR2A	chr1:61720273-61720897	MCF10A-Er-Src	breast:	n/a	n/a
10	USF1	chr1:61720408-61720801	H1-hESC	embryonic stem cell:	n/a	chr1:61720624-61720640
11	FOS	chr1:61720346-61720761	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr1:61720282-61720671	MCF10A-Er-Src	breast:	n/a	n/a
13	KAP1	chr1:61720555-61721187	U2OS	brain:	n/a	n/a
14	FOS	chr1:61720310-61720700	MCF10A-Er-Src	breast:	n/a	n/a
15	USF1	chr1:61720451-61720744	H1-hESC	embryonic stem cell:	n/a	chr1:61720624-61720640
16	SIN3AK20	chr1:61720523-61720722	PFSK-1	brain:	n/a	n/a
17	FOXP2	chr1:61720557-61721028	SK-N-MC	brain:	n/a	n/a
18	USF2	chr1:61720375-61720711	Hela-S3	cervix:	n/a	chr1:61720624-61720640

No.	Distal block	Cell Line	Cell type
1	chr1:61518677..61520785-chr1:61719829..61722787,3	K562	blood:
2	chr1:61719954..61722883-chr1:61726240..61727822,2	K562	blood:
3	chr1:61546491..61548608-chr1:61718284..61720951,3	K562	blood:

Variant related genes	Relation type
ENSG00000237853	TF binding region
ENSG00000162599	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17121798	0.80[CEU][hapmap]
rs17121833	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs17121835	0.80[CEU][hapmap]
rs17121845	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17305204	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17305218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17311684	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17377134	1.00[ASW][hapmap];0.80[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17377148	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17377218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17377232	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17377267	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17377274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17377281	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17377295	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17377351	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74086705	0.91[EUR][1000 genomes]
rs74090339	0.91[EUR][1000 genomes]
rs74090351	0.91[EUR][1000 genomes]
rs7515011	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs868110	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9970076	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61715600-61725200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:61716000-61725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:61718400-61721000	Enhancers	HepG2	liver
4	chr1:61718400-61721200	Enhancers	Liver	Liver
5	chr1:61718600-61721200	Enhancers	Hela-S3	cervix
6	chr1:61718800-61721200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:61718800-61721600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:61718800-61721800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:61719400-61721200	Enhancers	A549	lung
10	chr1:61719400-61721600	Weak transcription	Lung	lung
11	chr1:61719400-61737200	Weak transcription	Esophagus	oesophagus
12	chr1:61719800-61721400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:61720000-61720800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:61720000-61720800	Enhancers	Stomach Mucosa	stomach
15	chr1:61720200-61720800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:61720200-61720800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:61720200-61720800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:61720200-61720800	Enhancers	Brain Germinal Matrix	brain
19	chr1:61720200-61720800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:61720200-61720800	Weak transcription	Small Intestine	intestine
21	chr1:61720200-61721000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:61720200-61721000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:61720200-61721000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:61720200-61721000	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr1:61720200-61721000	Active TSS	Fetal Muscle Trunk	muscle
26	chr1:61720200-61721000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:61720200-61721000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:61720200-61721000	Flanking Active TSS	HMEC	breast
29	chr1:61720200-61721000	Flanking Active TSS	K562	blood
30	chr1:61720200-61721200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:61720200-61721200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr1:61720200-61721200	Flanking Active TSS	Fetal Lung	lung
33	chr1:61720200-61721200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr1:61720200-61721200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:61720200-61721200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr1:61720200-61721200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr1:61720200-61721200	Flanking Active TSS	Osteobl	bone
38	chr1:61720200-61721400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:61720200-61721400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr1:61720200-61721400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:61720200-61721600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:61720200-61721600	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr1:61720200-61721800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:61720200-61721800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:61720200-61721800	Flanking Active TSS	NHEK	skin
46	chr1:61720400-61720800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:61720400-61720800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:61720400-61720800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:61720400-61720800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:61720400-61720800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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