Variant report

Variant	rs2973086
Chromosome Location	chr5:37751672-37751673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37750239..37752814-chr5:37754556..37757334,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1019505	0.87[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10461983	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10461984	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10941361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11749343	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11749345	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12513493	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12517792	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12519774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12521092	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12651803	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12656733	0.89[ASW][hapmap];1.00[YRI][hapmap]
rs13154033	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13159969	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13171010	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13182737	0.85[CHB][hapmap]
rs13185923	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13187416	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1363925	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1862577	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2973053	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2973088	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4431371	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4869542	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs581376	1.00[YRI][hapmap]
rs6897494	0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs870100	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9292665	0.89[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2973086	GDNF	cis	cerebellum	SCAN
rs2973086	LIFR	cis	parietal	SCAN
rs2973086	SLC1A3	cis	parietal	SCAN
rs2973086	RXFP3	cis	cerebellum	SCAN
rs2973086	OXCT1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37717800-37756200	Weak transcription	Right Ventricle	heart
2	chr5:37718400-37755800	Weak transcription	Spleen	Spleen
3	chr5:37721400-37764200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:37728000-37757200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:37728000-37758800	Weak transcription	Brain Germinal Matrix	brain
6	chr5:37728800-37754400	Weak transcription	Placenta	Placenta
7	chr5:37729400-37753200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:37729600-37755800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:37730200-37752000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:37730200-37757000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:37730400-37752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:37736200-37752200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:37736200-37752400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:37737800-37754000	Weak transcription	Left Ventricle	heart
15	chr5:37738400-37757200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:37738800-37756400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr5:37738800-37757400	Weak transcription	Brain Anterior Caudate	brain
18	chr5:37739000-37757200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:37739200-37757600	Weak transcription	A549	lung
20	chr5:37739400-37752800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:37739600-37757200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:37740800-37756200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:37741200-37757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:37742400-37753200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:37742800-37753400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:37743600-37752400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:37743800-37754800	Weak transcription	Liver	Liver
28	chr5:37744200-37753200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:37744200-37755000	Weak transcription	Ovary	ovary
30	chr5:37744200-37755800	Weak transcription	Gastric	stomach
31	chr5:37744200-37757200	Weak transcription	Dnd41	blood
32	chr5:37744200-37769200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:37744400-37751800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:37744600-37754000	Weak transcription	Fetal Stomach	stomach
35	chr5:37744600-37754400	Weak transcription	Aorta	Aorta
36	chr5:37744600-37754600	Weak transcription	Primary T cells from cord blood	blood
37	chr5:37744600-37755400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr5:37744600-37756800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr5:37744600-37757000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:37744600-37769400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:37745200-37757400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:37748000-37754600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:37748600-37753000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:37748800-37760000	Weak transcription	Fetal Brain Female	brain
45	chr5:37749600-37753600	Weak transcription	Adipose Nuclei	Adipose
46	chr5:37749600-37756800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr5:37750000-37755600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:37750200-37757800	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:37750800-37756800	Weak transcription	Brain Angular Gyrus	brain
50	chr5:37751000-37752400	Enhancers	NHDF-Ad	bronchial

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