Variant report

Variant	rs829638
Chromosome Location	chr2:30738382-30738383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30727521..30729274-chr2:30737533..30740125,3	K562	blood:
2	chr2:30733241..30735304-chr2:30736147..30738560,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11686191	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11892635	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1252639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252643	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252647	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1614348	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1662941	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1662942	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1662944	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662949	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662955	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662958	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1723156	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1723167	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1723170	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1723175	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462562	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2692041	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28538173	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35418935	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952124	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952148	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72853154	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562645	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829562	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829570	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829571	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829573	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829576	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829577	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829579	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829584	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829623	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829636	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs829645	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829647	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829648	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829649	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829650	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829651	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829658	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829686	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829687	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829638	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs829638	LYCAT	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30721400-30739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:30726200-30742600	Weak transcription	Pancreas	Pancrea
3	chr2:30727800-30741400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:30728000-30739200	Weak transcription	Thymus	Thymus
5	chr2:30729000-30741200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:30729000-30764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:30732000-30738400	Enhancers	K562	blood
8	chr2:30732000-30739400	Enhancers	Fetal Heart	heart
9	chr2:30732800-30742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:30733000-30756000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:30734000-30739000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:30734800-30739200	Weak transcription	Fetal Intestine Small	intestine
13	chr2:30734800-30741600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:30734800-30742200	Weak transcription	Gastric	stomach
15	chr2:30734800-30764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:30735000-30741400	Weak transcription	Primary T cells from cord blood	blood
17	chr2:30735000-30741600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:30735000-30741800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:30735000-30742600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:30735000-30742600	Weak transcription	HSMMtube	muscle
21	chr2:30735400-30739000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:30735400-30741600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:30735400-30741600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:30735400-30741800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:30735400-30742200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:30735400-30742200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:30735400-30742600	Weak transcription	Fetal Intestine Large	intestine
28	chr2:30735600-30740800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:30735600-30741400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:30735600-30742800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:30736600-30738800	Enhancers	Fetal Lung	lung
32	chr2:30736800-30739000	Weak transcription	Right Atrium	heart
33	chr2:30736800-30739000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:30736800-30752400	Weak transcription	Psoas Muscle	Psoas
35	chr2:30737000-30738400	Enhancers	Fetal Kidney	kidney
36	chr2:30737000-30738400	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr2:30737000-30738400	Enhancers	Fetal Stomach	stomach
38	chr2:30737000-30738400	Enhancers	Hela-S3	cervix
39	chr2:30737000-30742400	Weak transcription	Left Ventricle	heart
40	chr2:30737600-30740400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:30737600-30742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:30737800-30740000	Weak transcription	Small Intestine	intestine
43	chr2:30737800-30741800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:30737800-30742600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:30738000-30738400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:30738000-30738600	Enhancers	A549	lung
47	chr2:30738000-30739000	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:30738000-30740200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:30738000-30741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:30738000-30741600	Weak transcription	Fetal Thymus	thymus

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