Variant report

Variant	rs7161403
Chromosome Location	chr14:39898349-39898350
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	chr14:39649512..39652193-chr14:39897469..39900946,3	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10133417	0.82[JPT][hapmap]
rs10137352	0.82[JPT][hapmap]
rs10137905	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap]
rs10162550	0.82[JPT][hapmap]
rs11157058	0.81[JPT][hapmap]
rs11620695	0.82[JPT][hapmap]
rs11627580	0.81[JPT][hapmap]
rs11847057	0.81[ASN][1000 genomes]
rs12232110	0.93[ASN][1000 genomes]
rs12434140	0.87[CHB][hapmap]
rs12587625	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587713	0.82[JPT][hapmap]
rs12588110	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588175	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588483	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12589427	0.82[ASN][1000 genomes]
rs12590172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880644	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12882250	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883652	0.87[ASN][1000 genomes]
rs12886769	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12894855	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12896502	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12897960	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1594842	0.82[JPT][hapmap]
rs17109073	0.82[JPT][hapmap]
rs17109296	0.83[CHB][hapmap]
rs17109300	0.82[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs1950336	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1950338	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955703	0.90[AFR][1000 genomes]
rs1955718	0.83[ASN][1000 genomes]
rs1955729	0.83[CHB][hapmap]
rs2038278	0.87[ASN][1000 genomes]
rs2057137	0.82[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs2057138	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2207291	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274396	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs2415549	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415550	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899888	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2899889	0.93[ASN][1000 genomes]
rs34432449	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34649642	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34928332	0.80[ASN][1000 genomes]
rs35115885	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35459433	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35553183	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35693868	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35876588	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36010374	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899245	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899277	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899278	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902528	0.87[CHB][hapmap]
rs4902569	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4902570	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4902598	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902599	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902622	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902636	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902637	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902648	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902665	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902676	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902692	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs56046902	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67439322	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67963654	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs71407788	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71407789	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7140983	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7142748	0.92[AFR][1000 genomes]
rs7143646	0.80[JPT][hapmap]
rs7145821	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7148150	0.82[JPT][hapmap]
rs7148377	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7152341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7152935	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153413	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718364	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs719455	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs72675487	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003397	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8003621	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8004716	0.82[JPT][hapmap]
rs8006123	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8006321	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs910370	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910371	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332387	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7161403	LRFN5	cis	cerebellum	SCAN
rs7161403	PPP2R3C	cis	parietal	SCAN
rs7161403	CTAGE5	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
3	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
4	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:39887000-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:39889600-39898800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:39889800-39898800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:39891000-39898400	Weak transcription	Fetal Kidney	kidney
10	chr14:39891200-39898800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr14:39891800-39898800	Weak transcription	Aorta	Aorta
12	chr14:39891800-39898800	Weak transcription	Gastric	stomach
13	chr14:39891800-39898800	Weak transcription	Ovary	ovary
14	chr14:39891800-39898800	Weak transcription	Right Ventricle	heart
15	chr14:39891800-39899000	Weak transcription	Fetal Intestine Small	intestine
16	chr14:39891800-39899000	Weak transcription	Small Intestine	intestine
17	chr14:39893000-39899400	Weak transcription	Fetal Intestine Large	intestine
18	chr14:39893600-39898800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:39894400-39898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:39894400-39898800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr14:39894800-39898800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr14:39895400-39898800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr14:39895400-39898800	Enhancers	Dnd41	blood
24	chr14:39895800-39899000	Weak transcription	Spleen	Spleen
25	chr14:39896000-39898400	Weak transcription	NHEK	skin
26	chr14:39896000-39898600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr14:39896000-39898800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:39896000-39898800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:39896000-39898800	Weak transcription	NHDF-Ad	bronchial
30	chr14:39896000-39899000	Weak transcription	Placenta	Placenta
31	chr14:39896000-39899800	Weak transcription	HSMM	muscle
32	chr14:39896000-39900000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:39896000-39900200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr14:39896200-39898400	Weak transcription	HMEC	breast
35	chr14:39896200-39898600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr14:39896200-39898600	Weak transcription	Fetal Lung	lung
37	chr14:39896200-39898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr14:39896200-39898800	Weak transcription	Fetal Thymus	thymus
39	chr14:39896200-39898800	Weak transcription	Psoas Muscle	Psoas
40	chr14:39896200-39898800	Weak transcription	Thymus	Thymus
41	chr14:39896200-39898800	Weak transcription	HSMMtube	muscle
42	chr14:39896200-39899000	Weak transcription	Right Atrium	heart
43	chr14:39896200-39899200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr14:39896200-39899200	Weak transcription	Fetal Muscle Leg	muscle
45	chr14:39896400-39898600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr14:39896400-39898800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr14:39896400-39898800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr14:39896400-39898800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr14:39896400-39898800	Weak transcription	Osteobl	bone
50	chr14:39896400-39899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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