Variant report

Variant	rs7250409
Chromosome Location	chr19:38418878-38418879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr19:38418436-38420252	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:38418764-38419703	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:38418279-38419787	Raji	blood:	n/a	n/a
4	RUNX3	chr19:38418436-38419005	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:38418869-38419778	GM12892	blood:	n/a	n/a
6	RUNX3	chr19:38418559-38419796	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38417337..38419728-chr19:38472151..38473762,2	MCF-7	breast:

Variant related genes	Relation type
SIPA1L3	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10401637	0.84[EUR][1000 genomes]
rs10402530	0.81[EUR][1000 genomes]
rs10404567	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10420891	0.81[EUR][1000 genomes]
rs10427125	0.81[EUR][1000 genomes]
rs1119229	0.88[CEU][hapmap]
rs11879180	0.81[EUR][1000 genomes]
rs1291	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[TSI][hapmap]
rs12974225	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs12975057	0.81[EUR][1000 genomes]
rs1643462	0.86[EUR][1000 genomes]
rs1643463	0.86[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643467	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643469	0.89[EUR][1000 genomes]
rs1725477	0.86[EUR][1000 genomes]
rs1725478	0.86[EUR][1000 genomes]
rs1725480	0.86[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1725483	0.86[EUR][1000 genomes]
rs1725485	0.86[EUR][1000 genomes]
rs1725487	0.86[EUR][1000 genomes]
rs1725488	0.85[EUR][1000 genomes]
rs1725494	0.88[EUR][1000 genomes]
rs1725499	0.88[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs241932	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2544718	0.88[EUR][1000 genomes]
rs3095726	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs35209753	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353398	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353399	0.91[EUR][1000 genomes]
rs353400	0.91[EUR][1000 genomes]
rs353402	0.91[EUR][1000 genomes]
rs353403	0.89[EUR][1000 genomes]
rs353404	0.91[EUR][1000 genomes]
rs353407	0.91[EUR][1000 genomes]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353415	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs353416	0.91[EUR][1000 genomes]
rs353417	0.91[EUR][1000 genomes]
rs353419	0.91[EUR][1000 genomes]
rs353420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353421	0.91[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353424	0.91[EUR][1000 genomes]
rs353425	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353426	0.89[EUR][1000 genomes]
rs353427	0.91[EUR][1000 genomes]
rs353428	0.86[EUR][1000 genomes]
rs353429	0.84[EUR][1000 genomes]
rs353430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3786869	0.87[CEU][hapmap]
rs4239516	0.87[CEU][hapmap]
rs4802135	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4803524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4803551	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs4803573	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705491	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs705493	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705495	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705500	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7250571	0.84[EUR][1000 genomes]
rs7250868	0.84[EUR][1000 genomes]
rs7252010	0.83[EUR][1000 genomes]
rs7258597	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs752878	0.86[EUR][1000 genomes]
rs8101858	0.81[EUR][1000 genomes]
rs8102579	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs8107341	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8112706	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.81[EUR][1000 genomes]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs833896	0.85[EUR][1000 genomes]
rs833897	0.86[EUR][1000 genomes]
rs833898	0.86[EUR][1000 genomes]
rs833914	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs833926	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs856300	0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs856304	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs9304572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7250409	PHLDB3	cis	parietal	SCAN
rs7250409	ZNF571	cis	multi-tissue	Pritchard
rs7250409	DMPK	cis	parietal	SCAN
rs7250409	PAFAH1B3	cis	cerebellum	SCAN
rs7250409	PHLDB3	cis	cerebellum	SCAN
rs7250409	WDR87	cis	Thyroid	GTEx
rs7250409	AXL	cis	cerebellum	SCAN
rs7250409	CBLC	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
6	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
10	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:38399800-38421200	Weak transcription	Gastric	stomach
12	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
13	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
14	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:38400000-38422000	Weak transcription	HSMM	muscle
16	chr19:38400400-38419400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:38400400-38421800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr19:38400600-38422000	Weak transcription	HSMMtube	muscle
19	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
20	chr19:38400800-38422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:38401000-38421600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:38401200-38421200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
24	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
25	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:38406000-38419400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:38406000-38422600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr19:38406400-38419200	Weak transcription	Colonic Mucosa	Colon
29	chr19:38410200-38422200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:38410200-38422400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:38410400-38422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:38411600-38419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:38411600-38422600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:38411800-38421200	Weak transcription	NHEK	skin
35	chr19:38411800-38422200	Weak transcription	Brain Angular Gyrus	brain
36	chr19:38411800-38422200	Weak transcription	NH-A	brain
37	chr19:38411800-38422600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:38412000-38419800	Weak transcription	HepG2	liver
40	chr19:38412000-38422000	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:38412000-38422600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:38412000-38423800	Weak transcription	Lung	lung
43	chr19:38412200-38419400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:38412200-38419400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:38412200-38419600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:38412200-38421000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:38412200-38422600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:38412200-38422800	Weak transcription	Adipose Nuclei	Adipose
49	chr19:38412200-38423000	Weak transcription	Thymus	Thymus
50	chr19:38412400-38421200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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