Variant report

Variant	rs11951738
Chromosome Location	chr5:178491228-178491229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178483141..178486203-chr5:178488375..178491712,3	MCF-7	breast:
2	chr5:178486677..178489431-chr5:178490895..178493650,2	MCF-7	breast:
3	chr5:178487796..178490140-chr5:178490313..178493225,2	MCF-7	breast:
4	chr5:178490747..178493004-chr5:178499608..178501771,2	K562	blood:

Variant related genes	Relation type
ENSG00000177932	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10479519	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10479520	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10516149	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10516150	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11505147	0.84[ASN][1000 genomes]
rs11957976	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11958355	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11960161	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12152869	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13160086	0.96[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13161528	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13188724	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13359549	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359570	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359572	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13361077	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17078988	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17078991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047354	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2132671	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2132672	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34054398	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34431447	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34881171	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35568336	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797615	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4700780	1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4700781	0.90[ASN][1000 genomes]
rs4701030	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs4701045	0.89[ASN][1000 genomes]
rs58827878	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60061283	0.91[ASN][1000 genomes]
rs60073676	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62393072	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62393074	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62393075	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62393076	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601007	0.94[CEU][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6601010	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6859576	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6859767	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6860309	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861539	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6867119	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6867208	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868893	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6875473	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875622	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6880315	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6888539	0.86[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6888567	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6890317	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6891216	1.00[JPT][hapmap]
rs7707587	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7708743	0.94[ASN][1000 genomes]
rs7709054	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711420	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7732719	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7733072	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11951738	DKFZp686E2433	cis	Lymphoblastoid	GTEx
rs11951738	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL
rs11951738	LOC345462	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178487000-178497600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr5:178488000-178493000	ZNF genes & repeats	Fetal Intestine Small	intestine
3	chr5:178488200-178493200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:178488200-178493200	ZNF genes & repeats	Fetal Stomach	stomach
5	chr5:178488200-178511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:178488400-178492200	Strong transcription	Fetal Lung	lung
7	chr5:178488400-178492400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:178488400-178492600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:178488400-178492800	Weak transcription	HUVEC	blood vessel
10	chr5:178488400-178492800	Weak transcription	NHEK	skin
11	chr5:178488400-178497400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
12	chr5:178488400-178497800	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr5:178488400-178499000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:178488400-178508400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr5:178488400-178511600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:178488400-178512000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:178488600-178492600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:178488600-178492800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:178488600-178492800	Weak transcription	Brain Angular Gyrus	brain
20	chr5:178488600-178496200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr5:178488600-178497600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:178488600-178497800	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr5:178488600-178499400	ZNF genes & repeats	Fetal Brain Female	brain
24	chr5:178488600-178517200	ZNF genes & repeats	Liver	Liver
25	chr5:178488800-178492200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:178488800-178492200	Weak transcription	HSMMtube	muscle
27	chr5:178488800-178492400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:178488800-178492800	Weak transcription	Colonic Mucosa	Colon
29	chr5:178488800-178493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:178488800-178493400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:178489000-178491600	ZNF genes & repeats	Fetal Brain Male	brain
32	chr5:178489000-178491800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr5:178489000-178491800	Strong transcription	Thymus	Thymus
34	chr5:178489000-178492200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:178489000-178494800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:178489000-178495600	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr5:178489000-178496600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:178489000-178497000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:178489000-178497600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:178489200-178491400	Strong transcription	Fetal Intestine Large	intestine
41	chr5:178489200-178491400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:178489200-178491800	Strong transcription	Placenta	Placenta
43	chr5:178489200-178492600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:178489200-178493600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:178489200-178493800	Strong transcription	Brain Anterior Caudate	brain
46	chr5:178489200-178494000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:178489200-178495800	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr5:178489400-178492200	Weak transcription	NHDF-Ad	bronchial
49	chr5:178489400-178494200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:178489400-178511400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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