Variant report

Variant	rs968304
Chromosome Location	chr1:169094100-169094101
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169082965..169084504-chr1:169093592..169095304,2	MCF-7	breast:
2	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:
3	chr1:169087143..169088781-chr1:169092217..169094524,2	K562	blood:
4	chr1:169092696..169095785-chr1:169096212..169101951,6	MCF-7	breast:
5	chr1:169092445..169095068-chr1:169098832..169100908,2	K562	blood:
6	chr1:169087281..169089561-chr1:169092217..169094257,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10081959	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10800407	0.82[CHB][hapmap]
rs10919064	0.80[CEU][hapmap]
rs10919065	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919066	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919073	0.82[CHB][hapmap]
rs11809180	0.82[CHB][hapmap]
rs1200154	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1200157	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200159	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1200160	0.80[CEU][hapmap]
rs12023291	0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs12070626	1.00[CHB][hapmap]
rs12079745	0.82[CHB][hapmap]
rs12082618	0.82[CHB][hapmap]
rs12083075	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12084964	0.82[CHB][hapmap]
rs12086983	0.82[CHB][hapmap]
rs12095171	0.82[CHB][hapmap]
rs12128543	0.82[CEU][hapmap]
rs12129969	0.88[CHB][hapmap]
rs12145939	0.82[CHB][hapmap]
rs12354315	0.82[CHB][hapmap]
rs12691502	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs12724494	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12728466	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs12758208	0.82[CHB][hapmap]
rs1320965	0.82[CHB][hapmap]
rs1320966	0.82[CHB][hapmap]
rs1320967	0.82[CHB][hapmap]
rs1358712	0.82[CHB][hapmap]
rs1419322	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1419323	0.82[CHB][hapmap]
rs1892094	0.81[CEU][hapmap]
rs2143287	0.82[CHB][hapmap]
rs2420009	0.84[ASN][1000 genomes]
rs2901029	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753293	0.84[ASN][1000 genomes]
rs3766053	0.82[CHB][hapmap]
rs3766055	0.82[CHB][hapmap]
rs3766058	0.85[ASN][1000 genomes]
rs4656177	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4656179	0.84[ASN][1000 genomes]
rs4656651	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs4656652	0.84[ASN][1000 genomes]
rs58585501	0.85[ASN][1000 genomes]
rs6664272	0.85[ASN][1000 genomes]
rs7416619	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7552484	0.82[CHB][hapmap]
rs9633334	0.90[CHD][hapmap]
rs9804101	0.85[ASN][1000 genomes]
rs9887857	0.82[CHB][hapmap]
rs9988604	0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs968304	NME7	cis	Thyroid	GTEx
rs968304	NME7	cis	Artery Tibial	GTEx
rs968304	NME7	cis	Nerve Tibial	GTEx
rs968304	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169094600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169081000-169098200	Weak transcription	Small Intestine	intestine
4	chr1:169082200-169097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:169082400-169097400	Weak transcription	Fetal Thymus	thymus
6	chr1:169083600-169094600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:169085400-169097600	Weak transcription	Fetal Brain Male	brain
9	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:169085600-169094800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:169085600-169096600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:169085800-169097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
14	chr1:169086200-169094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
17	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:169086600-169095400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:169087800-169094400	Weak transcription	Colonic Mucosa	Colon
23	chr1:169089200-169096600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:169089600-169094600	Weak transcription	Osteobl	bone
25	chr1:169089600-169101600	Genic enhancers	A549	lung
26	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:169089800-169094400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:169089800-169096200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:169090000-169098200	Weak transcription	NHDF-Ad	bronchial
30	chr1:169090000-169098400	Weak transcription	HSMMtube	muscle
31	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:169090400-169103200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:169090600-169098400	Strong transcription	HSMM	muscle
34	chr1:169091000-169094200	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:169091000-169102200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:169091000-169102200	Strong transcription	HepG2	liver
37	chr1:169091000-169102800	Strong transcription	Hela-S3	cervix
38	chr1:169091200-169124600	Weak transcription	NHLF	lung
39	chr1:169091400-169094600	Enhancers	Fetal Heart	heart
40	chr1:169091400-169098400	Weak transcription	Aorta	Aorta
41	chr1:169091400-169102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:169091400-169103200	Strong transcription	Liver	Liver
43	chr1:169091400-169103400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:169091600-169094600	Weak transcription	Right Ventricle	heart
45	chr1:169091600-169095000	Weak transcription	Ovary	ovary
46	chr1:169091600-169097800	Weak transcription	Psoas Muscle	Psoas
47	chr1:169091600-169101200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:169091600-169102000	Weak transcription	Pancreas	Pancrea
49	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
50	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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