Variant report

Variant	rs3180770
Chromosome Location	chr19:19105773-19105774
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	POLR2A	chr19:19104506-19105785	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:19104289-19106900	K562	blood:	n/a	n/a
3	POLR2A	chr19:19105761-19105956	K562	blood:	n/a	n/a
4	POLR2A	chr19:19105768-19106987	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:
2	chr19:19080045..19082039-chr19:19105020..19106814,2	MCF-7	breast:
3	chr19:19104797..19106786-chr19:19215223..19218180,2	K562	blood:

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000064607	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000269131	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1007483	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10221504	0.92[ASN][1000 genomes]
rs10403222	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10404627	0.92[ASN][1000 genomes]
rs10405189	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405635	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10409164	0.92[ASN][1000 genomes]
rs10410451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10410568	0.92[ASN][1000 genomes]
rs10414676	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10416783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10417974	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10422335	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10422906	0.92[ASN][1000 genomes]
rs10423742	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10423815	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1079543	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10854005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1124921	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11666340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11670204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670239	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11671696	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11878368	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975676	0.92[ASN][1000 genomes]
rs12975754	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12976302	0.89[ASN][1000 genomes]
rs12978822	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12979565	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12982014	0.87[AMR][1000 genomes]
rs12985799	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1859267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2012318	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2107263	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158320	0.97[ASN][1000 genomes]
rs2240094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240095	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269806	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2269869	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2285851	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2313736	1.00[ASN][1000 genomes]
rs2872394	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808172	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4808179	0.97[ASN][1000 genomes]
rs4808184	0.92[ASN][1000 genomes]
rs4808900	0.81[AMR][1000 genomes]
rs4808902	1.00[ASN][1000 genomes]
rs4808904	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808905	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808907	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808911	0.97[ASN][1000 genomes]
rs4808913	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808916	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6511010	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511011	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6511014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511015	0.97[ASN][1000 genomes]
rs6511017	0.97[ASN][1000 genomes]
rs6511018	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6511021	0.85[CHB][hapmap]
rs7248399	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7248771	0.92[ASN][1000 genomes]
rs7250131	0.92[ASN][1000 genomes]
rs7253244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255937	0.92[ASN][1000 genomes]
rs7256648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7257635	0.88[ASN][1000 genomes]
rs7258637	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259510	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs757220	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8101529	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103431	0.92[ASN][1000 genomes]
rs8104799	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106146	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107710	0.87[ASN][1000 genomes]
rs8109654	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110629	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112566	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916898	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs929215	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304959	0.97[ASN][1000 genomes]
rs9676917	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3180770	ZNF506	cis	parietal	SCAN
rs3180770	TMEM161A	cis	Muscle Skeletal	GTEx
rs3180770	SFRS14	cis	multi-tissue	Pritchard
rs3180770	SUGP1	cis	parietal	SCAN
rs3180770	SFRS14	Cis_1M	lymphoblastoid	RTeQTL
rs3180770	MED26	cis	cerebellum	SCAN
rs3180770	TSSK6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19098000-19106600	Weak transcription	Fetal Kidney	kidney
3	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:19100200-19105800	Strong transcription	Brain Inferior Temporal Lobe	brain
5	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
6	chr19:19100600-19106000	Strong transcription	Fetal Intestine Large	intestine
7	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:19100800-19106400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:19100800-19106400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:19100800-19106600	Strong transcription	Fetal Muscle Leg	muscle
11	chr19:19101000-19105800	Strong transcription	Brain Hippocampus Middle	brain
12	chr19:19101000-19106400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:19101000-19106400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:19101000-19106400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:19101000-19107200	Strong transcription	Esophagus	oesophagus
16	chr19:19101000-19109400	Strong transcription	Lung	lung
17	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
19	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
20	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
21	chr19:19101200-19106000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:19101200-19106200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr19:19101200-19106400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:19101200-19106400	Strong transcription	Brain Substantia Nigra	brain
25	chr19:19101200-19108200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr19:19101200-19108400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr19:19101200-19108400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:19101200-19109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:19101200-19110400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:19101400-19105800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:19101400-19106200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:19101400-19106200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:19101400-19106200	Strong transcription	Placenta	Placenta
39	chr19:19101400-19106200	Strong transcription	NHDF-Ad	bronchial
40	chr19:19101400-19106400	Strong transcription	Osteobl	bone
41	chr19:19101400-19106800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:19101400-19109800	Strong transcription	Liver	Liver
43	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr19:19101600-19106400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:19101600-19106800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr19:19101600-19107200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:19101600-19109400	Strong transcription	Adipose Nuclei	Adipose
50	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood

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