Variant report

Variant	rs2119937
Chromosome Location	chr15:56414697-56414698
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11629483	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631191	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905899	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907263	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12911094	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12911427	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914260	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12914640	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1372753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442640	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1829542	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249090	0.84[CEU][hapmap]
rs2414464	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460647	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2460648	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2460650	0.92[CEU][hapmap]
rs2682044	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2682046	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2682051	0.92[CEU][hapmap]
rs2682054	0.92[CEU][hapmap]
rs2682059	0.92[CEU][hapmap]
rs2713923	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2713924	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2713926	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2713933	0.92[CEU][hapmap]
rs2713935	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2713936	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2713938	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2713941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2718915	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2718921	0.89[YRI][hapmap]
rs2718934	0.92[CEU][hapmap]
rs2718941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2725854	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs2725870	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2947021	0.84[CEU][hapmap]
rs34044869	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34144128	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34224072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34386737	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756325	0.92[ASN][1000 genomes]
rs35082998	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35722267	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35749329	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35972806	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310791	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310792	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774231	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4774232	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774847	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59432349	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62044082	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62044110	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044111	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493835	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7165270	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168319	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174823	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175745	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7176107	0.88[CEU][hapmap]
rs7496025	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8024031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028353	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029114	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032242	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8033653	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672886	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672928	0.83[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2119937	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2119937	RFX7	cis	lung	GTEx
rs2119937	RFX7	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
4	chr15:56388800-56441600	Weak transcription	Lung	lung
5	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:56389800-56415600	Weak transcription	Placenta	Placenta
8	chr15:56390600-56416400	Weak transcription	HUVEC	blood vessel
9	chr15:56390600-56417400	Weak transcription	Adipose Nuclei	Adipose
10	chr15:56390600-56418000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:56390800-56418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr15:56391800-56415800	Weak transcription	Ovary	ovary
13	chr15:56392600-56417200	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:56394000-56418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:56394200-56417000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:56394800-56414800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:56395000-56415800	Weak transcription	Fetal Thymus	thymus
18	chr15:56395000-56418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:56405800-56414800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:56408000-56418200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:56409400-56418400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:56410800-56419400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:56411400-56424000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:56411600-56436800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:56411800-56418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:56411800-56419600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:56412000-56418200	Weak transcription	Gastric	stomach
28	chr15:56412200-56420400	Weak transcription	Colonic Mucosa	Colon
29	chr15:56412400-56423200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
30	chr15:56412600-56416000	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr15:56412600-56419600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:56412600-56422000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:56412800-56415200	ZNF genes & repeats	HepG2	liver
34	chr15:56412800-56415600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:56412800-56418400	Weak transcription	Psoas Muscle	Psoas
36	chr15:56413000-56415400	Weak transcription	Brain Angular Gyrus	brain
37	chr15:56413000-56417600	Weak transcription	NHEK	skin
38	chr15:56413200-56423800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr15:56413400-56415200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr15:56413400-56416200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:56413400-56416200	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr15:56413400-56418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:56413400-56419400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr15:56413400-56441600	Weak transcription	Spleen	Spleen
45	chr15:56413600-56421800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:56413800-56414800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
47	chr15:56413800-56418400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:56413800-56418400	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:56414000-56417200	Strong transcription	HMEC	breast
50	chr15:56414000-56418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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