Variant report

Variant	rs590540
Chromosome Location	chr15:42467550-42467551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42467304..42469217-chr15:42478721..42481700,2	K562	blood:
2	chr15:42463650..42465546-chr15:42466316..42468360,2	K562	blood:
3	chr15:42456428..42459201-chr15:42465437..42468242,2	K562	blood:

Variant related genes	Relation type
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10152909	0.84[ASN][1000 genomes]
rs11070363	0.84[ASN][1000 genomes]
rs12324804	0.84[ASN][1000 genomes]
rs12440779	0.81[ASN][1000 genomes]
rs12442769	0.84[ASN][1000 genomes]
rs12915387	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12915946	0.84[ASN][1000 genomes]
rs12917071	0.84[ASN][1000 genomes]
rs1616957	0.92[ASN][1000 genomes]
rs1619537	0.92[ASN][1000 genomes]
rs1626437	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1630294	0.88[ASN][1000 genomes]
rs1678987	0.88[ASN][1000 genomes]
rs1678988	0.88[ASN][1000 genomes]
rs1678989	0.88[ASN][1000 genomes]
rs1678990	0.88[ASN][1000 genomes]
rs1678995	0.98[ASN][1000 genomes]
rs1678996	0.98[ASN][1000 genomes]
rs1679000	0.98[ASN][1000 genomes]
rs1679001	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679008	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679011	0.84[ASN][1000 genomes]
rs1703748	0.98[ASN][1000 genomes]
rs1703751	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1703753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712390	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1712391	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712397	0.92[ASN][1000 genomes]
rs1712406	0.92[ASN][1000 genomes]
rs1712407	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712408	0.84[ASN][1000 genomes]
rs1712409	0.84[ASN][1000 genomes]
rs1712410	0.84[ASN][1000 genomes]
rs1712417	0.88[ASN][1000 genomes]
rs1712420	0.88[ASN][1000 genomes]
rs1712422	0.92[ASN][1000 genomes]
rs1712442	0.92[ASN][1000 genomes]
rs2412671	0.98[ASN][1000 genomes]
rs2412674	0.92[ASN][1000 genomes]
rs2620378	0.98[ASN][1000 genomes]
rs2620379	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620380	0.98[ASN][1000 genomes]
rs2620381	0.90[ASN][1000 genomes]
rs2620383	0.92[ASN][1000 genomes]
rs2620387	0.84[ASN][1000 genomes]
rs2663092	0.98[ASN][1000 genomes]
rs2663093	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2663096	0.92[ASN][1000 genomes]
rs2677751	0.98[ASN][1000 genomes]
rs28767320	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2928333	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583208	0.86[EUR][1000 genomes]
rs4923934	0.84[ASN][1000 genomes]
rs4924633	0.88[ASN][1000 genomes]
rs4924635	0.84[ASN][1000 genomes]
rs4924636	0.88[ASN][1000 genomes]
rs4924638	0.84[ASN][1000 genomes]
rs583541	0.94[ASN][1000 genomes]
rs588695	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs593910	0.98[ASN][1000 genomes]
rs598441	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599316	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602270	0.98[ASN][1000 genomes]
rs603468	0.92[ASN][1000 genomes]
rs607959	0.92[ASN][1000 genomes]
rs609660	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613090	0.92[ASN][1000 genomes]
rs613131	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613157	0.98[ASN][1000 genomes]
rs614733	0.98[ASN][1000 genomes]
rs614774	0.98[ASN][1000 genomes]
rs615023	0.96[ASN][1000 genomes]
rs616071	0.98[ASN][1000 genomes]
rs618161	0.92[ASN][1000 genomes]
rs621365	0.98[ASN][1000 genomes]
rs627478	0.98[ASN][1000 genomes]
rs629255	0.98[ASN][1000 genomes]
rs633310	0.88[ASN][1000 genomes]
rs633483	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635617	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635669	0.98[ASN][1000 genomes]
rs635690	0.98[ASN][1000 genomes]
rs635919	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636604	0.98[ASN][1000 genomes]
rs637445	0.98[ASN][1000 genomes]
rs638240	0.92[ASN][1000 genomes]
rs641119	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644627	0.98[ASN][1000 genomes]
rs645304	0.98[ASN][1000 genomes]
rs647581	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648720	0.94[ASN][1000 genomes]
rs650910	0.98[ASN][1000 genomes]
rs652192	0.92[ASN][1000 genomes]
rs659354	0.92[ASN][1000 genomes]
rs660033	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663454	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665262	0.98[ASN][1000 genomes]
rs665718	0.98[ASN][1000 genomes]
rs668973	0.98[ASN][1000 genomes]
rs670329	0.98[ASN][1000 genomes]
rs670421	0.98[ASN][1000 genomes]
rs672946	0.98[ASN][1000 genomes]
rs677845	0.98[ASN][1000 genomes]
rs677895	0.98[ASN][1000 genomes]
rs683227	0.92[ASN][1000 genomes]
rs683579	0.92[ASN][1000 genomes]
rs685521	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181577	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023923	0.92[ASN][1000 genomes]
rs8030650	0.84[ASN][1000 genomes]
rs8031735	0.88[ASN][1000 genomes]
rs8036917	0.84[ASN][1000 genomes]
rs8108	0.92[ASN][1000 genomes]
rs9783720	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590540	LRRC57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42449000-42481800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:42449600-42468200	Strong transcription	Fetal Brain Female	brain
3	chr15:42450200-42468600	Strong transcription	Fetal Stomach	stomach
4	chr15:42450200-42472400	Strong transcription	Fetal Intestine Small	intestine
5	chr15:42450400-42468400	Strong transcription	Primary T cells from cord blood	blood
6	chr15:42450400-42468400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr15:42450400-42476600	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:42450600-42468000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:42450600-42468200	Strong transcription	Brain Germinal Matrix	brain
10	chr15:42450600-42479800	Weak transcription	Psoas Muscle	Psoas
11	chr15:42450600-42485000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:42450600-42486200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:42450600-42487400	Strong transcription	Primary B cells from cord blood	blood
14	chr15:42450800-42471400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:42450800-42484000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:42450800-42485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:42450800-42485200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:42451000-42468600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:42451000-42471000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:42451000-42479600	Strong transcription	Liver	Liver
21	chr15:42451000-42484000	Strong transcription	Placenta	Placenta
22	chr15:42451000-42484400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:42451000-42484800	Strong transcription	Fetal Intestine Large	intestine
24	chr15:42451000-42484800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:42451000-42485000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:42451000-42485000	Strong transcription	Thymus	Thymus
27	chr15:42451000-42487600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr15:42451200-42468200	Strong transcription	Aorta	Aorta
29	chr15:42451200-42468600	Strong transcription	Osteobl	bone
30	chr15:42451200-42473800	Strong transcription	Brain Anterior Caudate	brain
31	chr15:42451200-42474800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:42451200-42484800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:42451200-42484800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:42451200-42485800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:42451200-42486200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr15:42451200-42487600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr15:42451400-42468200	Strong transcription	Brain Angular Gyrus	brain
38	chr15:42451400-42468400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:42451400-42469400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:42451400-42473400	Strong transcription	Fetal Lung	lung
41	chr15:42451400-42484400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:42451400-42484800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:42451400-42485000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:42451600-42468200	Strong transcription	HSMMtube	muscle
45	chr15:42451600-42468400	Strong transcription	Dnd41	blood
46	chr15:42451800-42485000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:42452000-42470800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:42452000-42473400	Strong transcription	NH-A	brain
49	chr15:42452200-42484800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:42452200-42484800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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