Variant report

Variant	rs3745195
Chromosome Location	chr19:40842529-40842530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40842267..40845117-chr19:40949082..40951268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167565	Chromatin interaction
ENSG00000268366	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11083554	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12151335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459567	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12460555	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12460615	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12977474	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12985477	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16974196	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1962639	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1991460	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304186	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs2368575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33933140	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs34894858	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs35562135	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3746006	0.81[JPT][hapmap]
rs4479364	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4490097	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4502340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524046	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802072	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4803324	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803325	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803326	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803327	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803328	0.86[ASN][1000 genomes]
rs55710016	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57158010	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58502633	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59263025	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259273	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259541	0.85[JPT][hapmap]
rs73046335	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7507651	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508513	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110323	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs890773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892117	0.82[CHB][hapmap];0.91[JPT][hapmap]

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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3745195	SLC1A5	cis	parietal	SCAN
rs3745195	TMEM91	cis	parietal	SCAN
rs3745195	PLAUR	cis	cerebellum	SCAN
rs3745195	VASP	cis	cerebellum	SCAN
rs3745195	DMRTC2	cis	parietal	SCAN
rs3745195	ERCC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40820800-40848400	Strong transcription	Dnd41	blood
2	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:40822000-40843400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
5	chr19:40822200-40842600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:40822200-40843200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:40822200-40845400	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:40822400-40846200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:40823400-40845400	Strong transcription	Thymus	Thymus
10	chr19:40824000-40842600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:40824200-40846400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:40824200-40848600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr19:40824200-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr19:40824400-40843000	Strong transcription	Fetal Thymus	thymus
15	chr19:40825200-40842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:40825400-40842600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr19:40825800-40842600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:40825800-40842600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr19:40825800-40845400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr19:40826400-40843000	Strong transcription	Primary T cells from cord blood	blood
21	chr19:40826400-40847400	Weak transcription	Right Atrium	heart
22	chr19:40826600-40842800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:40826600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:40826800-40842800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:40827600-40845000	Strong transcription	GM12878-XiMat	blood
26	chr19:40829200-40843000	Strong transcription	Spleen	Spleen
27	chr19:40831400-40842600	Strong transcription	Primary B cells from cord blood	blood
28	chr19:40832200-40852800	Weak transcription	NHDF-Ad	bronchial
29	chr19:40833800-40846000	Weak transcription	Fetal Heart	heart
30	chr19:40834000-40842800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr19:40834400-40853400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr19:40834800-40845600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:40834800-40853600	Weak transcription	Small Intestine	intestine
34	chr19:40836000-40845600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:40836000-40853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:40836600-40842600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:40836600-40842600	Strong transcription	Fetal Intestine Small	intestine
38	chr19:40836600-40842800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:40836600-40842800	Strong transcription	Esophagus	oesophagus
40	chr19:40836600-40843000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr19:40836800-40842600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:40836800-40842600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:40837200-40848400	Weak transcription	Psoas Muscle	Psoas
44	chr19:40837400-40842600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr19:40837400-40847600	Weak transcription	Colonic Mucosa	Colon
46	chr19:40837400-40853400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:40837400-40853600	Weak transcription	Stomach Mucosa	stomach
48	chr19:40837600-40842800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:40837600-40847400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:40837800-40846600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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