Variant report

Variant	rs748344
Chromosome Location	chr15:56390616-56390617
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56389724..56392498-chr15:56393728..56396342,2	K562	blood:
2	chr15:56281435..56283774-chr15:56390486..56392704,2	MCF-7	breast:
3	chr15:56389724..56392748-chr15:56393728..56397126,3	K562	blood:
4	chr15:56386726..56388923-chr15:56388990..56391326,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10152826	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs10162834	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10163161	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632218	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11858173	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11858245	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909153	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13379820	0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238601	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819384	0.92[LWK][hapmap]
rs1829543	0.92[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2460649	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs2465405	0.80[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs2584689	0.92[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2682030	0.80[EUR][1000 genomes]
rs2682031	0.95[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs2682032	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682050	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap]
rs2713922	0.92[CEU][hapmap]
rs2713934	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2713937	0.92[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs2713939	0.80[EUR][1000 genomes]
rs2718924	0.92[CEU][hapmap]
rs2718934	0.83[CHB][hapmap]
rs2725871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2947023	0.80[EUR][1000 genomes]
rs34361729	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35840822	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274791	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60138831	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62044114	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493836	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7170102	0.85[EUR][1000 genomes]
rs8041422	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap]
rs894415	0.92[CEU][hapmap];0.86[TSI][hapmap];0.82[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
rs748344	RFXDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56381600-56391000	Strong transcription	HMEC	breast
2	chr15:56381600-56397000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:56382200-56399200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:56382600-56391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:56382800-56395800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:56383200-56395600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:56383400-56395200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:56383600-56391000	Strong transcription	NH-A	brain
9	chr15:56383800-56394200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:56383800-56398400	Strong transcription	Dnd41	blood
11	chr15:56384000-56390800	Strong transcription	Primary B cells from cord blood	blood
12	chr15:56384000-56395800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:56384200-56391200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:56384600-56395000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:56385000-56390800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:56385000-56394000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr15:56385000-56394800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:56385200-56391000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr15:56385400-56390800	Strong transcription	Primary T cells from cord blood	blood
20	chr15:56385400-56390800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:56385400-56391000	Strong transcription	A549	lung
22	chr15:56385400-56391000	Strong transcription	HepG2	liver
23	chr15:56385600-56391200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr15:56385600-56394000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:56385600-56394400	Strong transcription	Liver	Liver
26	chr15:56385600-56394800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:56385600-56405600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:56385800-56394000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:56386200-56390800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:56386200-56395000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:56386400-56397400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:56386600-56396200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr15:56387200-56390800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:56387400-56396000	Weak transcription	Fetal Heart	heart
35	chr15:56387600-56394000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:56388200-56391400	Weak transcription	Psoas Muscle	Psoas
37	chr15:56388400-56402000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:56388800-56392000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:56388800-56392000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:56388800-56392200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:56388800-56392200	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:56388800-56393400	Weak transcription	NHEK	skin
43	chr15:56388800-56396000	Weak transcription	Colonic Mucosa	Colon
44	chr15:56388800-56396200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:56388800-56396400	Weak transcription	Gastric	stomach
46	chr15:56388800-56396400	Weak transcription	Right Ventricle	heart
47	chr15:56388800-56396600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:56388800-56397400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:56388800-56398400	Weak transcription	Esophagus	oesophagus
50	chr15:56388800-56399000	Weak transcription	H9 Cell Line	embryonic stem cell

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