Variant report

Variant	rs10411176
Chromosome Location	chr19:37686953-37686954
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10401525	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10402050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10404069	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10405372	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10406612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10407224	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10410905	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10413304	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414983	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418314	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419174	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10422428	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10424841	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10425441	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10426093	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11084873	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12972146	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12975869	0.85[EUR][1000 genomes]
rs12978093	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12983153	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2385412	0.81[ASN][1000 genomes]
rs28462002	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28660259	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28701616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34915391	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35522655	0.84[ASN][1000 genomes]
rs4473303	0.89[ASN][1000 genomes]
rs4805198	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4805207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4805208	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806406	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4806414	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62108899	0.86[ASN][1000 genomes]
rs6510583	0.81[ASN][1000 genomes]
rs8101338	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8111936	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112011	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10411176	PAFAH1B3	cis	cerebellum	SCAN
rs10411176	DMPK	cis	parietal	SCAN
rs10411176	CBLC	cis	parietal	SCAN
rs10411176	XRCC1	cis	parietal	SCAN
rs10411176	LIPE	cis	cerebellum	SCAN
rs10411176	MEGF8	cis	cerebellum	SCAN
rs10411176	VASP	cis	parietal	SCAN
rs10411176	ZNF420	cis	lymphoblastoid	seeQTL
rs10411176	SNRPD2	cis	parietal	SCAN
rs10411176	EXOSC5	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37673200-37690600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr19:37675000-37701000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:37677200-37687600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
4	chr19:37679000-37700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:37680600-37700800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:37680800-37689800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:37680800-37695000	Weak transcription	HSMM	muscle
8	chr19:37680800-37700800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:37680800-37700800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:37681000-37687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:37681000-37690800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:37681000-37695800	Weak transcription	NH-A	brain
13	chr19:37681000-37695800	Weak transcription	NHLF	lung
14	chr19:37681000-37700800	Weak transcription	HSMMtube	muscle
15	chr19:37681000-37700800	Weak transcription	HUVEC	blood vessel
16	chr19:37681000-37701000	Weak transcription	Fetal Heart	heart
17	chr19:37681200-37696600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:37681600-37690600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:37682400-37688600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:37682800-37689200	Weak transcription	Right Ventricle	heart
21	chr19:37683200-37688800	Weak transcription	Primary B cells from cord blood	blood
22	chr19:37683200-37695200	Weak transcription	Brain Substantia Nigra	brain
23	chr19:37683400-37688600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:37683400-37688600	Weak transcription	Fetal Kidney	kidney
25	chr19:37683400-37688600	Strong transcription	Fetal Lung	lung
26	chr19:37683400-37688600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:37683400-37688800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:37683400-37690000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:37683400-37697400	Weak transcription	Fetal Brain Male	brain
30	chr19:37684600-37688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:37684600-37688600	Weak transcription	Brain Angular Gyrus	brain
32	chr19:37684600-37689200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:37684800-37687200	Weak transcription	Primary T cells from cord blood	blood
34	chr19:37684800-37688600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:37684800-37688800	Weak transcription	Thymus	Thymus
36	chr19:37684800-37690000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:37684800-37690200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:37685000-37687400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:37685000-37687800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr19:37685000-37688000	Weak transcription	Brain Anterior Caudate	brain
41	chr19:37685000-37688600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:37685000-37689200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:37685200-37687200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:37685200-37687400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:37685200-37688600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:37685200-37689800	Weak transcription	Fetal Brain Female	brain
47	chr19:37685400-37687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:37685400-37687400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:37685400-37688600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr19:37685400-37688600	Weak transcription	Brain Inferior Temporal Lobe	brain

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