Variant report

Variant	rs7714427
Chromosome Location	chr5:128454132-128454133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:128429580..128432261-chr5:128453645..128456486,2	MCF-7	breast:
2	chr5:128451572..128454294-chr5:128458058..128461292,3	K562	blood:
3	chr5:128446074..128449776-chr5:128450937..128454358,4	K562	blood:
4	chr17:57183686..57184258-chr5:128453625..128454242,2	MCF-7	breast:
5	chr5:128453538..128456511-chr5:128465200..128466831,2	MCF-7	breast:
6	chr4:78521675..78522522-chr5:128453764..128454552,2	K562	blood:

Variant related genes	Relation type
ENSG00000224738	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000066583	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10036277	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10058170	0.81[AMR][1000 genomes]
rs10071265	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1127827	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148740	1.00[LWK][hapmap]
rs1181965	1.00[LWK][hapmap]
rs1181966	1.00[LWK][hapmap]
rs11960471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112697	0.87[AMR][1000 genomes]
rs2161403	0.84[AMR][1000 genomes]
rs2194149	0.83[AMR][1000 genomes]
rs2312251	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2430194	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2430195	0.96[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs257911	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs257912	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs257919	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3798115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3798117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822830	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3822832	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4836444	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58498861	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6595879	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];1.00[ASN][1000 genomes]
rs6595885	0.84[AMR][1000 genomes]
rs6867600	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6868228	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881138	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6888909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7733245	0.83[AMR][1000 genomes]
rs963677	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv882842	chr5:128301971-128552706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription 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 miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv599701	chr5:128328165-128773052	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv882847	chr5:128368505-128665719	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv882848	chr5:128378225-128516629	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
6	nsv882849	chr5:128446692-128501738	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7714427	SHROOM1	cis	cerebellum	SCAN
rs7714427	SLC27A6	cis	parietal	SCAN
rs7714427	FNIP1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128431400-128457400	Weak transcription	Lung	lung
2	chr5:128431600-128454200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:128432200-128454600	Weak transcription	Aorta	Aorta
4	chr5:128434000-128455600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:128434000-128458400	Weak transcription	Esophagus	oesophagus
6	chr5:128434400-128454200	Weak transcription	Colonic Mucosa	Colon
7	chr5:128434400-128461800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:128434800-128461600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:128435200-128462200	Weak transcription	Pancreas	Pancrea
10	chr5:128439600-128456200	Weak transcription	Spleen	Spleen
11	chr5:128443000-128459800	Weak transcription	Fetal Kidney	kidney
12	chr5:128443600-128454400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:128443600-128454400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:128444000-128454200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:128444000-128455000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:128444000-128460200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:128444000-128461600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:128444000-128461600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:128444000-128462000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:128444000-128462400	Weak transcription	Gastric	stomach
21	chr5:128444600-128461600	Weak transcription	Fetal Intestine Small	intestine
22	chr5:128445000-128455400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:128446400-128456000	Weak transcription	Ovary	ovary
24	chr5:128446800-128454400	Weak transcription	Brain Anterior Caudate	brain
25	chr5:128447200-128454200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:128447400-128461600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:128447600-128455600	Weak transcription	GM12878-XiMat	blood
28	chr5:128448400-128454200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:128448600-128454400	Weak transcription	NHEK	skin
30	chr5:128448800-128461400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:128448800-128461600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:128448800-128461600	Weak transcription	Dnd41	blood
33	chr5:128449000-128454600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:128449000-128461400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:128449400-128457000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr5:128449400-128461200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:128449600-128460200	Weak transcription	Primary B cells from cord blood	blood
38	chr5:128452000-128460000	Weak transcription	Liver	Liver
39	chr5:128452400-128454200	Strong transcription	Adipose Nuclei	Adipose
40	chr5:128452800-128454800	Strong transcription	Primary T cells from cord blood	blood
41	chr5:128453000-128460600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:128453000-128461600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:128453200-128454200	Enhancers	Fetal Heart	heart
44	chr5:128453200-128454200	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:128453200-128454800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:128453200-128454800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr5:128453200-128461600	Weak transcription	Fetal Intestine Large	intestine
48	chr5:128453200-128462600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:128453400-128460000	Weak transcription	Left Ventricle	heart
50	chr5:128453600-128454200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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