Variant report

Variant	rs3737061
Chromosome Location	chr1:180931300-180931301
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	EGR1	chr1:180931290-180931785	MCF-7	breast:	n/a	chr1:180931528-180931539 chr1:180931528-180931538 chr1:180931526-180931540 chr1:180931528-180931538 chr1:180931522-180931544
2	EGR1	chr1:180931221-180931885	MCF-7	breast:	n/a	chr1:180931528-180931539 chr1:180931528-180931538 chr1:180931526-180931540 chr1:180931528-180931538 chr1:180931522-180931544

No.	Distal block	Cell Line	Cell type
1	chr1:180930763..180932787-chr1:181056794..181059196,2	MCF-7	breast:
2	chr1:180924358..180926561-chr1:180929794..180932663,2	K562	blood:
3	chr1:180921163..180924034-chr1:180930743..180932979,2	MCF-7	breast:
4	chr1:180929325..180932935-chr1:180990437..180993069,4	MCF-7	breast:
5	chr1:180924451..180927761-chr1:180928276..180933255,6	MCF-7	breast:
6	chr1:180931171..180933343-chr1:180934751..180937015,2	K562	blood:
7	chr1:180917532..180919530-chr1:180930414..180932412,2	K562	blood:
8	chr1:180920141..180924832-chr1:180927695..180934337,6	MCF-7	breast:
9	chr1:180917167..180919032-chr1:180930403..180931914,2	K562	blood:
10	chr1:180929617..180932008-chr1:180990364..180992961,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STX6-4	chr1:180931250-180931685	NONHSAT008276

Variant related genes	Relation type
ENSG00000251520	TF binding region
ENSG00000135823	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000232586	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10737352	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753230	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10914142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914143	0.84[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs10914145	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12145907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4651079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4652543	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59805843	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516077	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525223	0.82[ASN][1000 genomes]
rs7537859	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538053	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551728	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2754938	chr1:180919343-180934343	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180918600-180939800	Weak transcription	K562	blood
3	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:180919800-180935800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:180922600-180949400	Strong transcription	Dnd41	blood
6	chr1:180923000-180935800	Weak transcription	Fetal Heart	heart
7	chr1:180923600-180944800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
9	chr1:180923800-180933400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:180923800-180938600	Weak transcription	Aorta	Aorta
11	chr1:180923800-180942800	Weak transcription	Fetal Lung	lung
12	chr1:180923800-180944800	Weak transcription	HUVEC	blood vessel
13	chr1:180923800-180944800	Weak transcription	NH-A	brain
14	chr1:180924000-180932800	Weak transcription	Lung	lung
15	chr1:180924000-180933800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:180924000-180934000	Weak transcription	Spleen	Spleen
17	chr1:180924000-180934400	Weak transcription	Left Ventricle	heart
18	chr1:180924000-180935000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:180924000-180935600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:180924000-180937800	Weak transcription	Right Ventricle	heart
21	chr1:180924000-180938400	Weak transcription	NHLF	lung
22	chr1:180924000-180938800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:180924000-180939000	Weak transcription	Colonic Mucosa	Colon
24	chr1:180924000-180939200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:180924000-180939400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:180924000-180940000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:180924000-180940200	Weak transcription	Gastric	stomach
28	chr1:180924000-180941600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:180924200-180931400	Weak transcription	Osteobl	bone
30	chr1:180924200-180933400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:180924200-180934400	Weak transcription	GM12878-XiMat	blood
32	chr1:180924200-180935000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:180924200-180936200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:180924200-180939000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:180924200-180940000	Weak transcription	NHDF-Ad	bronchial
36	chr1:180924200-180941600	Weak transcription	Pancreas	Pancrea
37	chr1:180924200-180942000	Weak transcription	Liver	Liver
38	chr1:180924200-180943400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:180924400-180931400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:180924400-180934200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:180925400-180931400	Weak transcription	NHEK	skin
42	chr1:180926000-180931400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:180926000-180938200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:180926600-180937000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:180927000-180935400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:180927200-180931800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:180927600-180934400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:180928400-180931800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:180928400-180932000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:180928400-180932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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