Variant report

Variant	rs13141335
Chromosome Location	chr4:48414055-48414056
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	chr4:48409760..48411298-chr4:48411593..48414353,2	K562	blood:
2	chr4:48413445..48415846-chr4:48421918..48423637,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10000288	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10001054	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003458	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10004425	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024547	0.85[ASN][1000 genomes]
rs10517217	0.95[JPT][hapmap]
rs1055720	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1055721	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938530	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11731199	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11737752	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13122065	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17609600	0.84[ASN][1000 genomes]
rs17655838	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1876834	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28411210	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28464394	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28636546	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28659782	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28690347	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309890	0.90[JPT][hapmap]
rs4413478	0.85[JPT][hapmap]
rs4695376	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695382	0.88[AFR][1000 genomes]
rs6447631	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447632	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66894522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68142816	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6841390	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843652	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6853315	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7655066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7658851	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7662325	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7664981	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7668401	0.85[JPT][hapmap]
rs7688310	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700141	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9884339	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9992736	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9995939	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9999482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13141335	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
2	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:48385400-48422000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:48387000-48422200	Weak transcription	Colonic Mucosa	Colon
7	chr4:48387400-48424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:48387600-48431400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:48387800-48424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:48391000-48424800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:48391200-48423200	Weak transcription	NHLF	lung
12	chr4:48391200-48424600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:48391600-48434000	Weak transcription	Fetal Heart	heart
14	chr4:48395600-48424800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:48396200-48422000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:48397000-48424800	Weak transcription	Stomach Mucosa	stomach
17	chr4:48397400-48424000	Weak transcription	HUVEC	blood vessel
18	chr4:48398800-48423200	Weak transcription	GM12878-XiMat	blood
19	chr4:48399000-48422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:48399000-48423800	Weak transcription	NH-A	brain
21	chr4:48399000-48423800	Weak transcription	NHDF-Ad	bronchial
22	chr4:48399200-48422200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:48399200-48426000	Weak transcription	A549	lung
24	chr4:48399800-48424400	Weak transcription	Brain Anterior Caudate	brain
25	chr4:48400000-48431000	Weak transcription	Brain Angular Gyrus	brain
26	chr4:48400200-48423200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:48400200-48426600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:48404600-48421800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:48404800-48423600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:48405400-48422200	Weak transcription	Osteobl	bone
31	chr4:48405800-48421800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:48405800-48422200	Weak transcription	Fetal Thymus	thymus
33	chr4:48406000-48414800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:48406000-48422200	Weak transcription	Esophagus	oesophagus
35	chr4:48406000-48423800	Weak transcription	Fetal Brain Female	brain
36	chr4:48406000-48424600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:48406000-48424600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:48406200-48421400	Weak transcription	Fetal Intestine Small	intestine
39	chr4:48406200-48422000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:48406200-48422000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:48406200-48422200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:48406200-48422200	Weak transcription	Pancreas	Pancrea
43	chr4:48406200-48433200	Weak transcription	NHEK	skin
44	chr4:48408600-48416200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:48409400-48414400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:48411000-48414200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:48411200-48423000	Weak transcription	Hela-S3	cervix
48	chr4:48411400-48414800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:48411800-48424000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:48412000-48414200	Strong transcription	HSMM	muscle

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