Variant report

Variant	rs9292871
Chromosome Location	chr5:43304402-43304403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43296533..43300928-chr5:43302565..43304605,4	K562	blood:
2	chr5:43303994..43305958-chr5:43311700..43313713,2	MCF-7	breast:
3	chr5:43296533..43300517-chr5:43302565..43304936,4	K562	blood:
4	chr5:43119332..43123146-chr5:43304067..43307597,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112972	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10039048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap]
rs10462048	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap]
rs10512825	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10512827	0.89[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs10512828	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10805671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10805672	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10805673	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10805674	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs10805675	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10941620	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10941621	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10941622	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10941623	0.92[EUR][1000 genomes]
rs10941628	0.89[EUR][1000 genomes]
rs10941630	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10941631	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10941632	0.82[EUR][1000 genomes]
rs11738086	0.86[EUR][1000 genomes]
rs11739009	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11739665	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11740128	0.92[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11741246	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs11742171	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11742712	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11743622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743633	0.92[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs11746629	0.83[EUR][1000 genomes]
rs11747105	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11747834	0.89[EUR][1000 genomes]
rs11950040	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs11950448	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11951584	0.86[EUR][1000 genomes]
rs11956635	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11956936	0.83[EUR][1000 genomes]
rs11956988	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11960415	0.82[EUR][1000 genomes]
rs12109933	0.83[EUR][1000 genomes]
rs12189016	0.89[EUR][1000 genomes]
rs12189447	0.86[EUR][1000 genomes]
rs12513864	0.80[EUR][1000 genomes]
rs12514393	0.92[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12514399	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12515072	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs12516435	0.84[EUR][1000 genomes]
rs12517362	0.84[EUR][1000 genomes]
rs12518032	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12518127	0.89[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs12519554	0.92[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs12520012	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12520895	0.82[EUR][1000 genomes]
rs12522178	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13161494	0.86[ASN][1000 genomes]
rs13187876	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13659	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1545753	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1548097	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1564196	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1564197	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1564198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244818	0.92[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2086133	0.84[EUR][1000 genomes]
rs2126947	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2126948	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2126949	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2169781	0.89[EUR][1000 genomes]
rs2330150	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2330242	0.83[EUR][1000 genomes]
rs2330243	0.86[ASN][1000 genomes]
rs35231094	0.83[EUR][1000 genomes]
rs35239179	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3733768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733769	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4050485	0.86[EUR][1000 genomes]
rs4288122	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4320264	0.86[EUR][1000 genomes]
rs4373285	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4395639	0.92[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs4443425	0.85[EUR][1000 genomes]
rs4443426	0.96[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4574553	0.86[EUR][1000 genomes]
rs4591755	0.89[EUR][1000 genomes]
rs4866734	0.87[EUR][1000 genomes]
rs4866737	0.90[EUR][1000 genomes]
rs4866738	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4866741	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4866813	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4866818	0.92[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs4866820	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4866821	0.85[EUR][1000 genomes]
rs4866822	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4866824	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4866825	0.85[EUR][1000 genomes]
rs4866826	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55634155	0.89[EUR][1000 genomes]
rs55647314	0.86[EUR][1000 genomes]
rs55759097	0.80[EUR][1000 genomes]
rs55759722	0.84[EUR][1000 genomes]
rs55794239	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55800451	0.87[EUR][1000 genomes]
rs55992392	0.85[EUR][1000 genomes]
rs56023994	0.86[EUR][1000 genomes]
rs56029402	0.88[EUR][1000 genomes]
rs56071328	0.85[EUR][1000 genomes]
rs56114604	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56185290	0.85[EUR][1000 genomes]
rs56206275	0.86[EUR][1000 genomes]
rs57066570	0.85[EUR][1000 genomes]
rs57392430	0.88[EUR][1000 genomes]
rs57401732	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58358642	0.85[EUR][1000 genomes]
rs58679159	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58966636	0.85[EUR][1000 genomes]
rs59078439	0.86[EUR][1000 genomes]
rs59625262	0.85[EUR][1000 genomes]
rs59814709	0.86[EUR][1000 genomes]
rs60207549	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60445501	0.90[EUR][1000 genomes]
rs61627503	0.84[EUR][1000 genomes]
rs6451684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66585077	0.83[EUR][1000 genomes]
rs66691321	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66914803	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67415672	0.87[EUR][1000 genomes]
rs67497876	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67620667	0.83[EUR][1000 genomes]
rs67651757	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67817333	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6814	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6863246	0.86[EUR][1000 genomes]
rs6863360	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867954	0.82[EUR][1000 genomes]
rs6886499	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6887351	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6895805	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898398	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7445066	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs754527	0.93[CHB][hapmap]
rs7701391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701642	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap]
rs7704588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708779	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7714027	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7714919	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7716091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7720165	0.92[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7720681	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs7722781	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727047	0.85[CEU][hapmap]
rs7734293	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9292874	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790987	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9292871	NNT	Cis_1M	lymphoblastoid	RTeQTL
rs9292871	NNT	cis	parietal	SCAN
rs9292871	HMGCS1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43284200-43309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:43287000-43305000	Strong transcription	HUVEC	blood vessel
3	chr5:43288200-43312400	Weak transcription	Spleen	Spleen
4	chr5:43288600-43310000	Weak transcription	Aorta	Aorta
5	chr5:43294200-43312400	Weak transcription	Thymus	Thymus
6	chr5:43294600-43309400	Weak transcription	Lung	lung
7	chr5:43295600-43311800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:43297400-43312200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:43297400-43312400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:43297600-43311800	Weak transcription	Hela-S3	cervix
11	chr5:43297800-43304800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:43298600-43310200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:43298800-43306200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:43298800-43306200	Weak transcription	Fetal Kidney	kidney
15	chr5:43298800-43310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:43298800-43311600	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:43298800-43312400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:43299000-43304600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:43299000-43306400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:43299000-43307800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:43299000-43309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:43299000-43309400	Weak transcription	Gastric	stomach
23	chr5:43299000-43309800	Weak transcription	Colonic Mucosa	Colon
24	chr5:43299000-43312000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:43299000-43312200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:43299000-43312400	Weak transcription	Right Ventricle	heart
27	chr5:43299200-43309800	Weak transcription	Fetal Lung	lung
28	chr5:43299200-43310200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:43299400-43311800	Weak transcription	HSMM	muscle
30	chr5:43299400-43312600	Weak transcription	Placenta	Placenta
31	chr5:43300200-43311800	Weak transcription	Fetal Stomach	stomach
32	chr5:43300400-43312200	Weak transcription	Esophagus	oesophagus
33	chr5:43300400-43312200	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:43300400-43312200	Weak transcription	Fetal Thymus	thymus
35	chr5:43300400-43312400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:43300400-43312400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr5:43300600-43305000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:43300600-43309800	Weak transcription	HSMMtube	muscle
39	chr5:43300800-43309200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:43300800-43309600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:43300800-43312000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr5:43301000-43305000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:43301000-43305200	Weak transcription	Fetal Intestine Small	intestine
44	chr5:43301000-43309400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:43301000-43312000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:43301000-43312200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:43301800-43304600	Enhancers	Fetal Brain Male	brain
48	chr5:43301800-43304800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr5:43302000-43304800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:43302000-43306200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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