Variant report

Variant	rs688585
Chromosome Location	chr1:210501504-210501505
allele	A/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	USF1	chr1:210501415-210501673	HepG2	liver:	n/a	chr1:210501547-210501558
2	USF1	chr1:210501385-210501647	SK-N-SH_RA	brain:	n/a	chr1:210501547-210501558
3	USF1	chr1:210501346-210501685	SK-N-SH_RA	brain:	n/a	chr1:210501547-210501558
4	USF1	chr1:210501314-210501650	H1-hESC	embryonic stem cell:	n/a	chr1:210501547-210501558
5	KAP1	chr1:210501326-210504273	HEK293	kidney:	n/a	n/a
6	USF1	chr1:210501388-210501728	SK-N-SH	brain:	n/a	chr1:210501547-210501558
7	GATA3	chr1:210501438-210501687	SH-SY5Y	brain:	n/a	n/a
8	POLR2A	chr1:210501429-210503021	MCF10A-Er-Src	breast:	n/a	n/a
9	USF1	chr1:210501425-210501681	H1-hESC	embryonic stem cell:	n/a	chr1:210501547-210501558
10	GATA2	chr1:210501347-210501744	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210499300..210503346-chr1:210545682..210548805,5	K562	blood:
2	chr1:210497683..210507034-chr1:210544536..210549319,22	MCF-7	breast:
3	chr1:210498648..210506320-chr1:210545155..210548300,7	K562	blood:
4	chr1:210498783..210502429-chr1:210544443..210548917,7	MCF-7	breast:

Variant related genes	Relation type
HHAT	TF binding region
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12144593	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890302	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1999890	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2357432	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357433	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4292962	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56393518	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591238	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613047	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs624600	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs664614	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6688459	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs684045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694602	0.87[EUR][1000 genomes];0.88[ASN][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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210495200-210501600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:210495800-210501800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:210499200-210501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:210501000-210501600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:210501200-210501600	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:210501200-210501600	Enhancers	Primary T cells from cord blood	blood
7	chr1:210501200-210501600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:210501200-210501600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:210501200-210501600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:210501200-210501600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:210501200-210501600	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:210501200-210501800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:210501200-210501800	Enhancers	Fetal Heart	heart
14	chr1:210501200-210502000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:210501200-210502000	Flanking Active TSS	Colon Smooth Muscle	Colon
16	chr1:210501400-210501600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr1:210501400-210501600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:210501400-210501600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:210501400-210501600	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:210501400-210501600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr1:210501400-210501600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:210501400-210501600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:210501400-210501600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:210501400-210501600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:210501400-210501600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:210501400-210501600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:210501400-210501600	Enhancers	Adipose Nuclei	Adipose
28	chr1:210501400-210501600	Enhancers	Liver	Liver
29	chr1:210501400-210501600	Enhancers	Brain Angular Gyrus	brain
30	chr1:210501400-210501600	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:210501400-210501600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:210501400-210501600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:210501400-210501600	Enhancers	Duodenum Mucosa	Duodenum
34	chr1:210501400-210501600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:210501400-210501600	Enhancers	Fetal Intestine Small	intestine
36	chr1:210501400-210501600	Enhancers	Fetal Lung	lung
37	chr1:210501400-210501600	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:210501400-210501600	Enhancers	Fetal Muscle Leg	muscle
39	chr1:210501400-210501600	Enhancers	Fetal Thymus	thymus
40	chr1:210501400-210501600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr1:210501400-210501600	Active TSS	Rectal Smooth Muscle	rectum
42	chr1:210501400-210501600	Enhancers	Thymus	Thymus
43	chr1:210501400-210501600	Active TSS	HepG2	liver
44	chr1:210501400-210501800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:210501400-210501800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr1:210501400-210501800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:210501400-210501800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:210501400-210501800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:210501400-210501800	Enhancers	Colonic Mucosa	Colon
50	chr1:210501400-210501800	Active TSS	Esophagus	oesophagus

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