Variant report

Variant	rs6451699
Chromosome Location	chr5:43461400-43461401
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43458100..43461748-chr5:43479402..43482480,3	MCF-7	breast:
2	chr5:43460240..43463188-chr5:43481708..43484249,2	MCF-7	breast:
3	chr5:43442199..43444663-chr5:43460452..43462412,2	K562	blood:

Variant related genes	Relation type
ENSG00000151881	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10036954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10038545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053229	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10054519	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10055801	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs10059912	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10059993	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10065689	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10066408	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10068064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10074682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10461744	0.86[YRI][hapmap]
rs10462051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10472380	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10473310	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10473311	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11742171	0.83[JPT][hapmap]
rs11949083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12187908	0.85[JPT][hapmap]
rs12521249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs12697457	0.82[EUR][1000 genomes]
rs13356232	0.82[YRI][hapmap]
rs13359906	0.82[EUR][1000 genomes]
rs1366410	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1389868	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1389869	0.96[ASN][1000 genomes]
rs1389870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1593971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16873438	0.86[YRI][hapmap]
rs2131998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132001	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2132003	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437972	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3805722	0.85[YRI][hapmap]
rs3806870	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4072918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4072919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4074777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4331909	0.81[ASN][1000 genomes]
rs4386738	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4467713	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4535459	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs4866822	0.80[JPT][hapmap]
rs4866831	0.82[ASN][1000 genomes]
rs4866833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4866835	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55667604	0.82[EUR][1000 genomes]
rs55855322	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56008952	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56333629	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57403343	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57547662	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59001943	0.81[ASN][1000 genomes]
rs60297702	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451693	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6451695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6451696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6451697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451698	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs6451704	0.96[ASN][1000 genomes]
rs6451705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451712	0.81[ASN][1000 genomes]
rs66495712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67466542	0.88[ASN][1000 genomes]
rs6858942	0.96[ASN][1000 genomes]
rs6860493	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6862102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6866325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866802	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6869933	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6870018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6878770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs6885679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6891363	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6895327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6896693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72756535	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73100614	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs750583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs754301	0.82[CHB][hapmap]
rs7703662	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7705166	0.85[CHB][hapmap]
rs7708779	0.81[JPT][hapmap]
rs7710628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7713479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7715782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7718627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7732140	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7732656	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7736108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885189	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6451699	NNT	Cis_1M	lymphoblastoid	RTeQTL
rs6451699	NNT	cis	multi-tissue	Pritchard

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43433800-43483400	Weak transcription	Gastric	stomach
2	chr5:43440000-43462400	Weak transcription	Colonic Mucosa	Colon
3	chr5:43440800-43466400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:43440800-43466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:43441600-43466600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:43444000-43461400	Weak transcription	Spleen	Spleen
7	chr5:43444000-43463600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:43444000-43464400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:43444000-43467000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:43444000-43467000	Weak transcription	Left Ventricle	heart
11	chr5:43444000-43482600	Weak transcription	HMEC	breast
12	chr5:43444200-43467000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:43444200-43472600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:43444400-43463800	Weak transcription	Small Intestine	intestine
15	chr5:43444600-43463600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:43444600-43466800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:43444800-43466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:43444800-43482600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:43445200-43466800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:43446600-43461800	Weak transcription	Right Ventricle	heart
21	chr5:43448200-43467400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr5:43448200-43471800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:43448400-43466200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr5:43448800-43463000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:43453400-43466200	Weak transcription	Liver	Liver
26	chr5:43453800-43466200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:43453800-43482600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:43454000-43482400	Weak transcription	Osteobl	bone
29	chr5:43454800-43466200	Weak transcription	Adipose Nuclei	Adipose
30	chr5:43454800-43482800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:43456000-43462800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:43456000-43462800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:43457200-43466200	Weak transcription	A549	lung
34	chr5:43457600-43463600	Weak transcription	Esophagus	oesophagus
35	chr5:43458800-43461600	Strong transcription	HSMM	muscle
36	chr5:43459200-43462200	ZNF genes & repeats	Dnd41	blood
37	chr5:43459600-43466200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:43459800-43462200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:43459800-43462600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr5:43460000-43462200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:43460000-43462200	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr5:43460000-43462400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:43460200-43462200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:43460200-43462200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr5:43460200-43462400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr5:43460200-43462400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:43460200-43462400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:43460400-43461400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:43460400-43462600	Strong transcription	Hela-S3	cervix
50	chr5:43460400-43466200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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