Variant report

Variant	rs59683545
Chromosome Location	chr1:227071383-227071384
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	RCOR1	chr1:227070193-227071402	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227058393..227060106-chr1:227070481..227073137,2	MCF-7	breast:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1341281	1.00[EUR][1000 genomes]
rs1341282	1.00[EUR][1000 genomes]
rs16846590	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4520384	1.00[EUR][1000 genomes]
rs57594469	1.00[EUR][1000 genomes]
rs58698650	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58973334	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59692841	1.00[EUR][1000 genomes]
rs60294511	1.00[EUR][1000 genomes]
rs60560949	1.00[EUR][1000 genomes]
rs61103575	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61185121	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61674281	0.89[AFR][1000 genomes]
rs6426539	1.00[EUR][1000 genomes]
rs6426540	1.00[EUR][1000 genomes]
rs6671059	1.00[EUR][1000 genomes]
rs6675452	1.00[EUR][1000 genomes]
rs6677908	1.00[EUR][1000 genomes]
rs6678839	1.00[EUR][1000 genomes]
rs6678940	1.00[EUR][1000 genomes]
rs74139805	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74139806	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74139837	0.80[AFR][1000 genomes]
rs74139838	0.80[AFR][1000 genomes]
rs74139842	0.87[AFR][1000 genomes]
rs7522645	1.00[EUR][1000 genomes]
rs7523790	1.00[EUR][1000 genomes]
rs7525819	1.00[EUR][1000 genomes]
rs7555672	1.00[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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:227060400-227073800	Weak transcription	HepG2	liver
4	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
6	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
10	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:227064600-227073000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:227066200-227072200	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr1:227066800-227071400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:227067000-227071800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:227067000-227072000	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:227067200-227072000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr1:227067600-227071800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:227067800-227075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:227068200-227073400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:227068600-227074200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:227068800-227072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:227069400-227074400	Enhancers	Fetal Thymus	thymus
26	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
27	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:227069400-227087800	Weak transcription	HMEC	breast
29	chr1:227069400-227102800	Weak transcription	K562	blood
30	chr1:227069600-227071800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:227069600-227075000	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr1:227069800-227071400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:227069800-227071400	Flanking Active TSS	GM12878-XiMat	blood
34	chr1:227069800-227071600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:227069800-227072200	Enhancers	Stomach Mucosa	stomach
36	chr1:227069800-227074600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr1:227069800-227075000	Enhancers	Primary hematopoietic stem cells	blood
38	chr1:227069800-227075000	Genic enhancers	Fetal Muscle Leg	muscle
39	chr1:227070000-227071400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr1:227070000-227071400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:227070000-227071400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:227070000-227071600	Enhancers	Left Ventricle	heart
43	chr1:227070000-227072200	Enhancers	Fetal Kidney	kidney
44	chr1:227070000-227076400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:227070200-227071400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:227070200-227071400	Weak transcription	Gastric	stomach
48	chr1:227070200-227071600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:227070400-227071400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:227070400-227071400	Enhancers	NH-A	brain

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