Variant report

Variant	rs3893725
Chromosome Location	chr5:42951941-42951942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42950468..42952623-chr5:43006794..43010300,4	MCF-7	breast:
2	chr5:42949709..42952302-chr5:42999079..43000906,2	MCF-7	breast:
3	chr5:42930977..42933954-chr5:42950606..42953206,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF131-4	chr5:42950963-42959174	XLOC_004362

Variant related genes	Relation type
ENSG00000271788	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10036916	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10064003	0.88[CHB][hapmap]
rs10522	0.82[YRI][hapmap]
rs10941598	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10941604	0.81[JPT][hapmap]
rs10941605	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11743246	0.83[EUR][1000 genomes]
rs11747714	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13169690	0.81[ASW][hapmap];0.82[CHD][hapmap]
rs1542369	0.84[CHD][hapmap]
rs160709	0.81[ASW][hapmap];0.81[CHD][hapmap]
rs17300176	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs186323	0.81[ASN][1000 genomes]
rs186324	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs188693	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2100473	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs222060	0.81[ASW][hapmap];0.82[CHD][hapmap]
rs2329995	0.81[CHD][hapmap]
rs2432097	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2548334	0.93[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs2548336	0.96[CEU][hapmap];0.82[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548339	0.81[ASN][1000 genomes]
rs2548345	0.82[ASN][1000 genomes]
rs2548350	0.88[CHB][hapmap]
rs2548353	0.81[JPT][hapmap]
rs2548356	0.81[JPT][hapmap]
rs2548374	0.81[EUR][1000 genomes]
rs2548382	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2603620	0.81[ASN][1000 genomes]
rs2603625	0.80[EUR][1000 genomes]
rs2603630	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2603631	0.81[EUR][1000 genomes]
rs2603632	0.81[EUR][1000 genomes]
rs2603633	0.81[EUR][1000 genomes]
rs2603644	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2603649	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2603650	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2603656	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs2876993	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882295	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs309909	0.81[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs309912	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs309923	0.87[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs309924	0.82[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs309925	0.83[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs309926	0.84[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs309927	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs309938	0.80[EUR][1000 genomes]
rs309948	0.87[ASN][1000 genomes]
rs309950	0.93[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316414	0.84[CHD][hapmap]
rs3849696	0.82[EUR][1000 genomes]
rs3849697	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3909456	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4092293	0.82[CHD][hapmap]
rs4092294	0.81[ASW][hapmap];0.82[CHD][hapmap];0.81[YRI][hapmap]
rs6451660	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs6451662	0.81[ASW][hapmap];0.84[CHD][hapmap];0.82[YRI][hapmap]
rs6859096	0.83[EUR][1000 genomes]
rs6861491	0.81[AMR][1000 genomes]
rs6880163	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6882794	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6883097	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884740	0.82[EUR][1000 genomes]
rs6889150	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6889271	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6890457	0.83[CEU][hapmap]
rs6890469	0.81[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap]
rs6899257	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7715065	0.81[JPT][hapmap]
rs7733383	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9292862	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv968909	chr5:42903982-42953465	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	esv3346992	chr5:42921680-42970055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
13	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv528880	chr5:42940230-42967215	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv515883	chr5:42949688-42967215	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3893725	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42948600-42952200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:42948800-42953000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:42949000-42952200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr5:42949000-42952400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr5:42949000-42952400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr5:42949000-42952800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:42949000-42953600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr5:42949200-42952000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
9	chr5:42949200-42952400	Active TSS	Aorta	Aorta
10	chr5:42949200-42952800	Bivalent/Poised TSS	Psoas Muscle	Psoas
11	chr5:42949200-42953200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr5:42949400-42952400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:42949400-42952400	ZNF genes & repeats	HSMM	muscle
14	chr5:42949400-42952600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr5:42949800-42952600	Active TSS	Thymus	Thymus
16	chr5:42950200-42952400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr5:42950400-42952800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr5:42950400-42953000	Active TSS	NHDF-Ad	bronchial
19	chr5:42950600-42952200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
20	chr5:42950600-42952400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr5:42950600-42952400	Active TSS	Ovary	ovary
22	chr5:42950600-42952600	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr5:42950600-42952600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
24	chr5:42950600-42952800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:42950600-42952800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr5:42950600-42952800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
27	chr5:42950600-42952800	Active TSS	Osteobl	bone
28	chr5:42950600-42953200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
29	chr5:42950600-42953600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:42950600-42954200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:42950600-42954600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:42950800-42952000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr5:42950800-42952000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
34	chr5:42950800-42952000	Bivalent Enhancer	Fetal Brain Male	brain
35	chr5:42950800-42952600	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr5:42950800-42952600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr5:42950800-42952600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:42950800-42952800	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr5:42950800-42952800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:42950800-42952800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr5:42950800-42953000	Active TSS	Esophagus	oesophagus
42	chr5:42950800-42953400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:42951000-42952000	Active TSS	Primary B cells from peripheral blood	blood
44	chr5:42951000-42952000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
45	chr5:42951000-42952000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
46	chr5:42951000-42952000	ZNF genes & repeats	HMEC	breast
47	chr5:42951000-42952000	Flanking Active TSS	NHLF	lung
48	chr5:42951000-42952200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:42951000-42952600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr5:42951000-42952600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain

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