Variant report

Variant	rs1345778
Chromosome Location	chr5:40712797-40712798
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40678891..40680674-chr5:40712439..40714300,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTC33-2	chr5:40711696-40713273	NONHSAT101146

Variant related genes	Relation type
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1002424	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs10036575	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10038769	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10042750	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055925	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10065570	0.81[GIH][hapmap]
rs10071679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10074991	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs10078575	0.97[ASN][1000 genomes]
rs13361707	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs1692252	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2329353	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs28540420	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3805497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4509070	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957342	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57806386	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60770691	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860328	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6868517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs6872282	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6873054	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876367	0.81[GIH][hapmap]
rs6897169	0.99[ASN][1000 genomes]
rs7705504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7716285	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726270	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7730368	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs980093	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	esv3432300	chr5:40698244-40726882	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1345778	FGF10	cis	cerebellum	SCAN
rs1345778	RPL37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:40694800-40721000	Weak transcription	Thymus	Thymus
8	chr5:40695200-40715800	Weak transcription	Primary B cells from cord blood	blood
9	chr5:40695200-40727000	Weak transcription	HSMM	muscle
10	chr5:40699000-40720800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr5:40700800-40712800	Weak transcription	Gastric	stomach
12	chr5:40700800-40720600	Weak transcription	Left Ventricle	heart
13	chr5:40700800-40720800	Weak transcription	Spleen	Spleen
14	chr5:40700800-40722200	Weak transcription	Lung	lung
15	chr5:40701000-40720800	Weak transcription	Aorta	Aorta
16	chr5:40701000-40722200	Weak transcription	Esophagus	oesophagus
17	chr5:40702400-40715800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:40702800-40715200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:40704200-40714800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:40705600-40727000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:40706200-40715800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:40706400-40717600	Weak transcription	Adipose Nuclei	Adipose
23	chr5:40706400-40717600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:40706400-40719800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:40706400-40720600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:40706400-40720800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:40706400-40721000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:40707000-40720600	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:40707600-40720800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:40708400-40717600	Weak transcription	A549	lung
31	chr5:40709400-40721000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:40709600-40716200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr5:40709600-40716200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:40709600-40745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:40710400-40721400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:40710600-40716200	Weak transcription	Fetal Lung	lung
37	chr5:40710600-40720800	Weak transcription	Fetal Thymus	thymus
38	chr5:40710800-40720800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:40711000-40716200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:40711000-40719200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:40711000-40720600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:40711000-40720800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:40711200-40721000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr5:40711400-40712800	Strong transcription	Primary T cells from cord blood	blood
45	chr5:40711400-40716200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:40711600-40715200	Weak transcription	NHDF-Ad	bronchial
47	chr5:40711800-40712800	Enhancers	Fetal Kidney	kidney
48	chr5:40711800-40717400	Weak transcription	Fetal Intestine Large	intestine
49	chr5:40711800-40720600	Weak transcription	Psoas Muscle	Psoas
50	chr5:40712000-40714000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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