Variant report

Variant	rs6848073
Chromosome Location	chr4:48405391-48405392
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48404225..48407126-chr4:48409105..48411506,2	K562	blood:
2	chr4:48342039..48343742-chr4:48404432..48406234,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10003230	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10026398	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10029785	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1055721	0.90[YRI][hapmap]
rs10805168	0.89[ASN][1000 genomes]
rs10938534	0.86[JPT][hapmap]
rs1117010	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11945562	0.91[JPT][hapmap]
rs12503644	0.85[ASN][1000 genomes]
rs12507206	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511991	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645501	0.82[JPT][hapmap]
rs12645951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649527	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649528	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13105385	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13115295	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13133788	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13148849	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13150017	0.87[EUR][1000 genomes]
rs1352433	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1352434	0.88[ASN][1000 genomes]
rs1472967	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507865	0.86[JPT][hapmap]
rs1586540	0.92[ASN][1000 genomes]
rs1703973	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17575720	0.82[JPT][hapmap]
rs17656040	0.80[JPT][hapmap]
rs17656094	0.82[JPT][hapmap]
rs1948167	0.92[ASN][1000 genomes]
rs2029348	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291474	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353312	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353314	0.88[ASN][1000 genomes]
rs2353315	0.82[ASN][1000 genomes]
rs28409655	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34975258	0.82[ASN][1000 genomes]
rs35758434	0.92[ASN][1000 genomes]
rs372825	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs382335	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3828496	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs392187	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs404348	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404445	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs404656	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs411261	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs421336	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421833	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs429969	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs432927	0.82[EUR][1000 genomes]
rs445892	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs449376	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs450498	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4536901	0.86[JPT][hapmap]
rs4694895	0.92[ASN][1000 genomes]
rs4695391	0.86[JPT][hapmap]
rs62309425	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447634	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811148	0.82[JPT][hapmap]
rs6816010	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816352	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829705	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829716	0.91[JPT][hapmap]
rs6836010	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836632	0.91[JPT][hapmap]
rs6837335	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6844211	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848395	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7438704	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7654770	0.91[JPT][hapmap]
rs7664981	0.94[YRI][hapmap]
rs7668529	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7672892	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674269	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7678164	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678379	0.91[JPT][hapmap]
rs7679210	0.82[JPT][hapmap]
rs7683398	0.82[JPT][hapmap]
rs7693461	0.82[JPT][hapmap]
rs7697851	0.91[JPT][hapmap]
rs7700018	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs776591	0.82[JPT][hapmap]
rs923372	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923373	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291323	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937888	0.86[JPT][hapmap]
rs952289	0.82[JPT][hapmap]
rs974014	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974015	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974016	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs992423	0.91[JPT][hapmap]
rs9996532	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv528084	chr4:48387851-48413919	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6848073	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
2	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
3	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
4	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:48383200-48412000	Weak transcription	Fetal Brain Male	brain
8	chr4:48385200-48405400	Weak transcription	Pancreas	Pancrea
9	chr4:48385400-48422000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:48387000-48422200	Weak transcription	Colonic Mucosa	Colon
11	chr4:48387400-48424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:48387600-48431400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:48387800-48424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:48388200-48405400	Weak transcription	NHEK	skin
15	chr4:48391000-48412600	Weak transcription	Brain Substantia Nigra	brain
16	chr4:48391000-48424800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:48391200-48405400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:48391200-48423200	Weak transcription	NHLF	lung
19	chr4:48391200-48424600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:48391600-48434000	Weak transcription	Fetal Heart	heart
21	chr4:48395600-48424800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:48396200-48422000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:48396400-48412400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:48397000-48424800	Weak transcription	Stomach Mucosa	stomach
25	chr4:48397400-48424000	Weak transcription	HUVEC	blood vessel
26	chr4:48398800-48423200	Weak transcription	GM12878-XiMat	blood
27	chr4:48399000-48422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:48399000-48423800	Weak transcription	NH-A	brain
29	chr4:48399000-48423800	Weak transcription	NHDF-Ad	bronchial
30	chr4:48399200-48412600	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:48399200-48412600	Weak transcription	HSMMtube	muscle
32	chr4:48399200-48422200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:48399200-48426000	Weak transcription	A549	lung
34	chr4:48399400-48412600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:48399800-48405400	Weak transcription	Ovary	ovary
36	chr4:48399800-48405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:48399800-48410800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:48399800-48424400	Weak transcription	Brain Anterior Caudate	brain
39	chr4:48400000-48412600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:48400000-48431000	Weak transcription	Brain Angular Gyrus	brain
41	chr4:48400200-48412600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:48400200-48412600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:48400200-48412800	Weak transcription	Fetal Kidney	kidney
44	chr4:48400200-48423200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:48400200-48426600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:48400400-48407800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:48400400-48410000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr4:48400400-48412000	Weak transcription	HSMM	muscle
49	chr4:48401800-48405600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:48403800-48405400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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