Variant report

Variant	rs6969879
Chromosome Location	chr7:64023371-64023372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:63772917..63775872-chr7:64021942..64025037,3	MCF-7	breast:
2	chr7:64022429..64024303-chr7:64027221..64029382,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF117-5	chr7:64023303-64023400	NONHSAT121019
2	lnc-ZNF117-5	chr7:64023303-64023453	NONHSAT121021

Variant related genes	Relation type
ENSG00000235349	Chromatin interaction
ENSG00000234444	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11760623	0.83[EUR][1000 genomes]
rs11761642	0.83[EUR][1000 genomes]
rs11762751	0.85[EUR][1000 genomes]
rs11763268	0.82[CEU][hapmap]
rs11763547	0.83[EUR][1000 genomes]
rs11764145	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11764842	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11765236	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11767478	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11768668	0.83[EUR][1000 genomes]
rs11771181	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11771906	0.85[EUR][1000 genomes]
rs11772160	0.88[EUR][1000 genomes]
rs12113093	0.83[EUR][1000 genomes]
rs12113237	0.84[EUR][1000 genomes]
rs12113448	0.87[EUR][1000 genomes]
rs13247185	0.95[JPT][hapmap]
rs1446886	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs17540510	0.83[JPT][hapmap]
rs1810683	0.94[ASN][1000 genomes]
rs2862792	0.83[LWK][hapmap];0.92[YRI][hapmap]
rs2862795	1.00[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2862879	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902179	0.80[EUR][1000 genomes]
rs34764583	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs4718083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56351418	0.85[EUR][1000 genomes]
rs56799822	0.82[EUR][1000 genomes]
rs57198153	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58113403	0.85[EUR][1000 genomes]
rs58450777	0.83[EUR][1000 genomes]
rs58967958	0.83[EUR][1000 genomes]
rs58990166	0.82[EUR][1000 genomes]
rs59015730	0.82[EUR][1000 genomes]
rs59622152	0.82[EUR][1000 genomes]
rs61055703	0.87[EUR][1000 genomes]
rs6460154	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6460161	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6460162	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs6944803	0.80[EUR][1000 genomes]
rs6952579	1.00[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs6954330	0.81[EUR][1000 genomes]
rs6954460	0.81[EUR][1000 genomes]
rs6964427	0.82[EUR][1000 genomes]
rs6965883	0.85[EUR][1000 genomes]
rs6967116	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968279	0.81[EUR][1000 genomes]
rs6971827	0.87[EUR][1000 genomes]
rs6976217	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6977201	1.00[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6978561	0.85[EUR][1000 genomes]
rs73128768	0.80[EUR][1000 genomes]
rs73128770	0.80[EUR][1000 genomes]
rs73128772	0.80[EUR][1000 genomes]
rs73130733	0.80[EUR][1000 genomes]
rs73130741	0.82[EUR][1000 genomes]
rs73130748	0.81[EUR][1000 genomes]
rs73130750	0.82[EUR][1000 genomes]
rs73130757	0.82[EUR][1000 genomes]
rs73130760	0.83[EUR][1000 genomes]
rs73130769	0.83[EUR][1000 genomes]
rs73130774	0.83[EUR][1000 genomes]
rs73130775	0.83[EUR][1000 genomes]
rs73130779	0.83[EUR][1000 genomes]
rs73130787	0.88[EUR][1000 genomes]
rs73134703	0.88[EUR][1000 genomes]
rs7776937	0.80[EUR][1000 genomes]
rs7778593	0.92[CEU][hapmap]
rs7785818	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7787877	0.83[EUR][1000 genomes]
rs7788788	0.88[EUR][1000 genomes]
rs7792261	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7796427	0.94[ASN][1000 genomes]
rs7801917	0.80[EUR][1000 genomes]
rs7804897	0.88[EUR][1000 genomes]
rs7806288	1.00[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7806747	0.83[EUR][1000 genomes]
rs9918511	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9918574	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429759	chr7:63662150-64110550	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv429760	chr7:63687850-64110550	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv429761	chr7:63747498-64096138	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
7	nsv429762	chr7:63790450-64110550	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
9	nsv1031703	chr7:63839601-64225952	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
11	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv1023042	chr7:63956027-64116232	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv970855	chr7:63959414-64023731	ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
15	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
17	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
19	nsv1021893	chr7:63995601-64155027	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
20	nsv538892	chr7:63995601-64155027	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6969879	VKORC1L1	cis	cerebellum	SCAN
rs6969879	ZNF107	Cis_1M	lymphoblastoid	RTeQTL
rs6969879	ZNF679	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64021400-64024000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:64021800-64024200	Active TSS	Brain Anterior Caudate	brain
3	chr7:64021800-64024200	Active TSS	Hela-S3	cervix
4	chr7:64022000-64024000	Active TSS	Right Atrium	heart
5	chr7:64022200-64024000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:64022200-64024000	Active TSS	Dnd41	blood
7	chr7:64022400-64023800	Active TSS	Brain Angular Gyrus	brain
8	chr7:64022400-64023800	Active TSS	Right Ventricle	heart
9	chr7:64022400-64023800	Active TSS	HSMM	muscle
10	chr7:64022400-64024000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:64022400-64024000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:64022400-64024000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:64022400-64024000	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr7:64022400-64024000	Active TSS	Muscle Satellite Cultured Cells	--
15	chr7:64022400-64024000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:64022400-64024000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:64022400-64024000	Active TSS	Psoas Muscle	Psoas
18	chr7:64022400-64024000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr7:64022400-64024000	Active TSS	HMEC	breast
20	chr7:64022400-64024000	Active TSS	NHEK	skin
21	chr7:64022400-64024200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:64022400-64024200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:64022400-64024400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr7:64022400-64024400	Active TSS	Osteobl	bone
25	chr7:64022600-64023400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr7:64022600-64023400	Active TSS	Fetal Heart	heart
27	chr7:64022600-64023600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr7:64022600-64023600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:64022600-64023600	Active TSS	Primary T cells from cord blood	blood
30	chr7:64022600-64023600	Active TSS	Fetal Thymus	thymus
31	chr7:64022600-64023800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
32	chr7:64022600-64023800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr7:64022600-64023800	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr7:64022600-64023800	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr7:64022600-64023800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:64022600-64023800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr7:64022600-64023800	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr7:64022600-64023800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:64022600-64023800	Active TSS	Aorta	Aorta
40	chr7:64022600-64023800	Active TSS	Brain Cingulate Gyrus	brain
41	chr7:64022600-64023800	Active TSS	Brain Hippocampus Middle	brain
42	chr7:64022600-64023800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr7:64022600-64023800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:64022600-64023800	Active TSS	Fetal Lung	lung
45	chr7:64022600-64023800	Active TSS	Fetal Muscle Leg	muscle
46	chr7:64022600-64023800	Active TSS	Rectal Smooth Muscle	rectum
47	chr7:64022600-64023800	Active TSS	HSMMtube	muscle
48	chr7:64022600-64024000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:64022600-64024000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr7:64022600-64024000	Active TSS	iPS-18 Cell Line	embryonic stem cell

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