Variant report

Variant	rs13379820
Chromosome Location	chr15:56409206-56409207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56407805..56409350-chr15:56422499..56425257,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10162834	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10163161	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632218	0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853158	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11856691	0.80[AMR][1000 genomes]
rs11858173	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11858245	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899534	0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909153	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17238601	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1829543	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2247838	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2460649	0.83[EUR][1000 genomes]
rs2465405	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2465969	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2584689	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2682030	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2682031	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2682032	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682048	0.84[AMR][1000 genomes]
rs2682050	0.89[YRI][hapmap]
rs2682055	0.87[AMR][1000 genomes]
rs2713922	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2713934	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2713937	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2713939	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2718924	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725871	0.92[ASN][1000 genomes]
rs2947023	0.88[EUR][1000 genomes]
rs34361729	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35187662	0.82[AMR][1000 genomes]
rs35840822	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274791	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60138831	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62044114	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493836	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs748344	0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894415	0.85[AMR][1000 genomes];0.89[EUR][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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13379820	RFXDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56388800-56411600	Weak transcription	Fetal Stomach	stomach
2	chr15:56388800-56414400	Weak transcription	Thymus	Thymus
3	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
6	chr15:56388800-56441600	Weak transcription	Lung	lung
7	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:56389600-56414400	Weak transcription	HSMMtube	muscle
10	chr15:56389800-56415600	Weak transcription	Placenta	Placenta
11	chr15:56390400-56414400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:56390600-56412600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:56390600-56413200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:56390600-56414200	Weak transcription	Fetal Lung	lung
15	chr15:56390600-56414200	Weak transcription	Left Ventricle	heart
16	chr15:56390600-56414600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:56390600-56416400	Weak transcription	HUVEC	blood vessel
18	chr15:56390600-56417400	Weak transcription	Adipose Nuclei	Adipose
19	chr15:56390600-56418000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:56390800-56418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:56391000-56411800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:56391800-56415800	Weak transcription	Ovary	ovary
23	chr15:56392600-56417200	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:56393800-56412400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:56394000-56414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:56394000-56418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:56394200-56417000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:56394400-56411000	Weak transcription	Liver	Liver
29	chr15:56394400-56411600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:56394400-56414000	Weak transcription	HMEC	breast
31	chr15:56394400-56414200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:56394400-56414200	Weak transcription	NH-A	brain
33	chr15:56394800-56414800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:56395000-56411600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:56395000-56412600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:56395000-56415800	Weak transcription	Fetal Thymus	thymus
37	chr15:56395000-56418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:56395200-56414200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:56395600-56411400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:56396000-56412600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:56397000-56410600	Weak transcription	Psoas Muscle	Psoas
42	chr15:56397000-56414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:56397200-56414200	Weak transcription	Primary T cells from cord blood	blood
44	chr15:56397400-56412400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:56397400-56412600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:56398400-56413200	Weak transcription	Dnd41	blood
47	chr15:56399200-56412800	Weak transcription	HepG2	liver
48	chr15:56405200-56410800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:56405200-56411200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:56405400-56414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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