Variant report

Variant	rs4656177
Chromosome Location	chr1:169105636-169105637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169096516..169099051-chr1:169103916..169105981,2	K562	blood:
2	chr1:169101598..169103432-chr1:169104990..169106712,2	K562	blood:
3	chr1:169104511..169107059-chr1:169109794..169111882,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10081959	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800406	0.92[AFR][1000 genomes]
rs10919065	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10919066	0.82[ASN][1000 genomes]
rs1200154	0.83[ASN][1000 genomes]
rs1200157	0.84[ASN][1000 genomes]
rs1200159	0.83[ASN][1000 genomes]
rs12070626	1.00[CHB][hapmap]
rs12079745	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs12082618	0.86[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs12082810	0.92[AFR][1000 genomes]
rs12083075	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084793	0.86[YRI][hapmap]
rs12086665	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs12086983	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12129969	0.86[CHB][hapmap]
rs12135928	0.92[AFR][1000 genomes]
rs12137282	0.91[CEU][hapmap]
rs12143131	0.92[AFR][1000 genomes]
rs12145939	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12354315	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12691502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745732	0.92[AFR][1000 genomes]
rs12752748	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs12758208	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1320965	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1419322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419323	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1419324	0.92[AFR][1000 genomes]
rs17345107	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs17349222	0.83[CEU][hapmap]
rs2143287	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2179491	0.83[YRI][hapmap]
rs2420008	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs2420009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901029	1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3753293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766053	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3766054	0.92[AFR][1000 genomes]
rs3766055	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4656179	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656180	0.83[YRI][hapmap]
rs4656651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656653	0.92[AFR][1000 genomes]
rs7416619	0.88[AFR][1000 genomes]
rs745922	0.87[AFR][1000 genomes]
rs7552323	0.83[CEU][hapmap]
rs7552484	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs968304	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9887857	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9887903	0.92[AFR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4656177	NME7	cis	Heart Left Ventricle	GTEx
rs4656177	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs4656177	NME7	cis	Artery Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169091200-169124600	Weak transcription	NHLF	lung
3	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
4	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:169091600-169120600	Weak transcription	Lung	lung
6	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
7	chr1:169092400-169106200	Weak transcription	Gastric	stomach
8	chr1:169095000-169112600	Weak transcription	Stomach Mucosa	stomach
9	chr1:169095800-169106200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
11	chr1:169096800-169108600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:169097000-169130000	Weak transcription	Ovary	ovary
13	chr1:169097600-169108200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:169098800-169112200	Weak transcription	HSMM	muscle
15	chr1:169099400-169110400	Weak transcription	Osteobl	bone
16	chr1:169099400-169111200	Weak transcription	Aorta	Aorta
17	chr1:169099400-169112000	Weak transcription	Psoas Muscle	Psoas
18	chr1:169100000-169108600	Weak transcription	Fetal Intestine Small	intestine
19	chr1:169100800-169115000	Weak transcription	Small Intestine	intestine
20	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
21	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:169101000-169113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
24	chr1:169101200-169108600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:169101200-169113800	Weak transcription	Brain Germinal Matrix	brain
26	chr1:169101400-169105800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:169102000-169106000	Weak transcription	HUVEC	blood vessel
28	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:169102200-169108200	Weak transcription	HepG2	liver
30	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
31	chr1:169102800-169106800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:169102800-169107600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:169102800-169107800	Weak transcription	GM12878-XiMat	blood
34	chr1:169102800-169112600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:169102800-169114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:169103000-169108200	Weak transcription	Fetal Intestine Large	intestine
37	chr1:169103200-169111200	Weak transcription	Liver	Liver
38	chr1:169103200-169116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:169103200-169116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:169103400-169109200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:169103400-169109800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:169103400-169110600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:169103400-169110600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:169103600-169114000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:169104000-169110400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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