Variant report

Variant	rs1662945
Chromosome Location	chr2:30672858-30672859
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30659383..30661784-chr2:30671941..30674589,2	K562	blood:
2	chr2:30659383..30660987-chr2:30671941..30673568,2	K562	blood:
3	chr2:30672724..30675685-chr2:30694165..30695792,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1036941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11692096	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11901266	0.90[ASN][1000 genomes]
rs1252619	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252627	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1252632	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252633	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252634	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1252635	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1252642	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1252645	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1662943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723172	0.98[AFR][1000 genomes]
rs17395007	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17395091	0.89[ASN][1000 genomes]
rs2253299	0.92[ASN][1000 genomes]
rs2262947	0.84[ASN][1000 genomes]
rs2593436	0.83[ASN][1000 genomes]
rs2593473	0.92[ASN][1000 genomes]
rs2602796	0.84[ASN][1000 genomes]
rs2602803	0.92[ASN][1000 genomes]
rs2602809	0.81[ASN][1000 genomes]
rs2609919	0.84[ASN][1000 genomes]
rs57484347	0.88[AFR][1000 genomes]
rs57637161	0.88[AFR][1000 genomes]
rs711236	0.88[AFR][1000 genomes]
rs711241	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73922662	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7559747	0.92[ASN][1000 genomes]
rs829566	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829567	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829568	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs829621	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829624	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829625	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829633	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829640	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829643	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829652	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829656	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829657	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829674	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829676	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829678	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829683	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829685	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829688	0.88[AFR][1000 genomes]
rs829691	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829692	0.98[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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1662945	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671000-30674200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:30671000-30675600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:30671000-30675600	Weak transcription	Psoas Muscle	Psoas
4	chr2:30671000-30677400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:30671000-30678200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:30671000-30678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:30671000-30679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:30671000-30682000	Weak transcription	Aorta	Aorta
9	chr2:30671000-30685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:30671200-30678400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:30671200-30681200	Weak transcription	Right Atrium	heart
12	chr2:30671200-30688200	Weak transcription	HSMM	muscle
13	chr2:30671400-30673000	Enhancers	Liver	Liver
14	chr2:30671400-30673400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:30671400-30673800	Enhancers	Fetal Intestine Large	intestine
16	chr2:30671600-30673000	Weak transcription	Left Ventricle	heart
17	chr2:30671600-30673800	Enhancers	Fetal Intestine Small	intestine
18	chr2:30671600-30674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:30671600-30674400	Weak transcription	NHEK	skin
20	chr2:30671600-30675600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:30671600-30675600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:30671600-30676400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:30671600-30676800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:30671600-30678400	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:30671600-30678800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:30671600-30679000	Weak transcription	Lung	lung
27	chr2:30671600-30682000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:30671600-30682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:30671600-30683800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:30671600-30685600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:30671600-30688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:30671600-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:30671800-30673000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:30671800-30673600	Enhancers	HepG2	liver
38	chr2:30671800-30673800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr2:30671800-30675400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:30671800-30675600	Weak transcription	Fetal Brain Female	brain
41	chr2:30671800-30677400	Weak transcription	Small Intestine	intestine
42	chr2:30671800-30679600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:30671800-30679600	Weak transcription	Fetal Kidney	kidney
44	chr2:30671800-30681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:30672000-30673000	Weak transcription	Primary T cells from cord blood	blood
46	chr2:30672000-30673000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:30672000-30673000	Weak transcription	Fetal Thymus	thymus
48	chr2:30672000-30674200	Weak transcription	HMEC	breast
49	chr2:30672000-30674400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:30672000-30675600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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