Variant report

Variant	rs754690
Chromosome Location	chr14:56689221-56689222
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56675081..56677798-chr14:56689013..56691356,2	MCF-7	breast:
2	chr14:56686325..56689607-chr14:56690528..56694792,5	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1028972	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.94[EUR][1000 genomes]
rs1152473	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1152474	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes]
rs1152475	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1152476	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs1152481	0.94[EUR][1000 genomes]
rs1152483	0.94[EUR][1000 genomes]
rs1188692	0.94[EUR][1000 genomes]
rs1479752	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171411	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979420	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242385	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs242392	0.84[MEX][hapmap]
rs242393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs242395	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[EUR][1000 genomes]
rs242398	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242400	0.84[MEX][hapmap]
rs242406	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs242407	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs242410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs242414	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs242417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242419	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs242579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs242587	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs242592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[EUR][1000 genomes]
rs242593	0.94[EUR][1000 genomes]
rs242594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs34175054	0.94[EUR][1000 genomes]
rs375156	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs402332	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs429676	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4901649	0.84[MEX][hapmap]
rs6573087	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7140808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145410	0.92[ASN][1000 genomes]
rs7153057	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153858	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs753109	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs754689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899603	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[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	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs754690	SEMA3A	trans	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56662600-56693000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr14:56665400-56691600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:56673000-56694600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:56673400-56694600	Weak transcription	Primary B cells from cord blood	blood
5	chr14:56681200-56689600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:56682000-56689800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr14:56682200-56699200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr14:56683000-56689600	Enhancers	Adipose Nuclei	Adipose
9	chr14:56684200-56689400	Weak transcription	Esophagus	oesophagus
10	chr14:56684400-56689400	Weak transcription	Psoas Muscle	Psoas
11	chr14:56684400-56691800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr14:56684400-56692600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr14:56684600-56692400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:56686600-56691200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:56686800-56694200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr14:56686800-56702000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:56687000-56689400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr14:56687000-56689400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr14:56687000-56689600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:56687000-56689600	Enhancers	Brain Hippocampus Middle	brain
21	chr14:56687000-56690000	Weak transcription	Fetal Intestine Small	intestine
22	chr14:56687000-56690600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr14:56687000-56690600	Weak transcription	Fetal Intestine Large	intestine
24	chr14:56687000-56691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:56687000-56691000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:56687000-56691000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr14:56687000-56691000	Weak transcription	Small Intestine	intestine
28	chr14:56687000-56691400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr14:56687200-56690000	Enhancers	Ovary	ovary
30	chr14:56687200-56690400	Weak transcription	A549	lung
31	chr14:56687200-56691000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr14:56687200-56691600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr14:56687800-56690200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr14:56687800-56691000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr14:56687800-56694800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr14:56688000-56690800	Weak transcription	Fetal Kidney	kidney
37	chr14:56688000-56690800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr14:56688000-56707800	Weak transcription	Spleen	Spleen
39	chr14:56688200-56689400	Weak transcription	Pancreas	Pancrea
40	chr14:56688200-56689400	Weak transcription	Right Atrium	heart
41	chr14:56688200-56689400	Weak transcription	Right Ventricle	heart
42	chr14:56688200-56690600	Weak transcription	Fetal Brain Male	brain
43	chr14:56688200-56691600	Weak transcription	Gastric	stomach
44	chr14:56688200-56692400	Weak transcription	Lung	lung
45	chr14:56688200-56694200	Weak transcription	Left Ventricle	heart
46	chr14:56688400-56689400	Enhancers	Primary T cells from cord blood	blood
47	chr14:56688400-56691000	Weak transcription	Fetal Stomach	stomach
48	chr14:56688400-56691600	Weak transcription	Fetal Muscle Leg	muscle
49	chr14:56688400-56691800	Weak transcription	Brain Anterior Caudate	brain
50	chr14:56688400-56694200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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