Variant report

Variant	rs62309458
Chromosome Location	chr4:48433510-48433511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1015699	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10805168	0.89[EUR][1000 genomes]
rs11731383	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503644	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12507206	0.81[ASN][1000 genomes]
rs12511991	0.81[ASN][1000 genomes]
rs13115295	0.81[ASN][1000 genomes]
rs13150017	0.94[ASN][1000 genomes]
rs1352434	0.87[EUR][1000 genomes]
rs1488647	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1586540	0.88[EUR][1000 genomes]
rs16861305	0.88[ASN][1000 genomes]
rs1948167	0.88[EUR][1000 genomes]
rs2291474	0.81[ASN][1000 genomes]
rs2353314	0.85[EUR][1000 genomes]
rs2353315	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2353855	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34975258	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35758434	0.89[EUR][1000 genomes]
rs4694895	0.88[EUR][1000 genomes]
rs4695377	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695381	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62309455	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834339	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7438713	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62309458	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL
rs62309458	SLC10A4	cis	lung	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48391600-48434000	Weak transcription	Fetal Heart	heart
2	chr4:48422600-48433600	Weak transcription	Esophagus	oesophagus
3	chr4:48422600-48434400	Weak transcription	Brain Germinal Matrix	brain
4	chr4:48423400-48438200	Weak transcription	Fetal Intestine Small	intestine
5	chr4:48425200-48433800	Weak transcription	Stomach Mucosa	stomach
6	chr4:48425200-48441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:48425400-48438400	Weak transcription	HSMMtube	muscle
8	chr4:48425800-48434000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:48425800-48434200	Weak transcription	Thymus	Thymus
10	chr4:48425800-48438400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:48425800-48438600	Weak transcription	Fetal Intestine Large	intestine
12	chr4:48426000-48433600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:48426000-48433800	Weak transcription	Left Ventricle	heart
14	chr4:48426000-48438200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:48426000-48442000	Weak transcription	K562	blood
16	chr4:48427800-48433800	Weak transcription	Placenta	Placenta
17	chr4:48428000-48433600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:48429800-48433800	Weak transcription	Fetal Thymus	thymus
19	chr4:48430200-48434800	Weak transcription	HSMM	muscle
20	chr4:48430200-48438600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:48430400-48433800	Weak transcription	Aorta	Aorta
22	chr4:48430600-48434600	Weak transcription	Primary B cells from cord blood	blood
23	chr4:48431000-48433600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:48431000-48434400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:48431000-48438400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:48431200-48434200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr4:48431400-48433600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:48431400-48433800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:48431600-48434200	Enhancers	Primary T cells from cord blood	blood
30	chr4:48431600-48434200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr4:48431600-48434200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:48431800-48434000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr4:48431800-48434000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr4:48432000-48433600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:48432200-48433600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:48432400-48433800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:48432800-48434000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:48432800-48434200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr4:48433000-48434000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:48433000-48434200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr4:48433200-48433600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:48433200-48433800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:48433200-48434000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr4:48433200-48434200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:48433200-48434400	Enhancers	HMEC	breast
46	chr4:48433200-48434400	Enhancers	NHEK	skin
47	chr4:48433400-48433800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr4:48433400-48433800	Weak transcription	Gastric	stomach
49	chr4:48433400-48434000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr4:48433400-48434000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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