Variant report

Variant	rs6672589
Chromosome Location	chr1:169431170-169431171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:169430304-169431497	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:169429836-169432222	K562	blood:	n/a	n/a
3	POLR2A	chr1:169429397-169431229	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:169430475-169431993	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169430787..169432465-chr1:169513559..169515145,2	MCF-7	breast:

Variant related genes	Relation type
CCDC181	TF binding region
ENSG00000234437	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10158131	0.88[CHB][hapmap]
rs1028180	0.89[CHB][hapmap]
rs10737546	0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753786	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10800447	1.00[CEU][hapmap];0.94[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]
rs10919132	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs10919140	0.88[CHB][hapmap]
rs10919173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919174	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12121994	0.89[CHB][hapmap]
rs12143193	0.89[CHB][hapmap]
rs12145146	0.84[CHB][hapmap]
rs12145226	0.89[CHB][hapmap]
rs12733001	0.88[CHB][hapmap]
rs12733037	0.82[CHB][hapmap]
rs12733626	0.88[CHB][hapmap]
rs12752953	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs1400836	0.81[YRI][hapmap]
rs1517743	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1517744	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1517745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1517747	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1533518	0.89[CHB][hapmap]
rs16862081	0.89[CHB][hapmap]
rs16862097	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs16862176	0.89[CHB][hapmap]
rs16862180	0.89[CHB][hapmap]
rs16862217	0.82[CHB][hapmap]
rs1883167	0.89[CHB][hapmap]
rs2037249	0.89[CHB][hapmap]
rs2066001	0.89[CHB][hapmap]
rs2271762	0.89[CHB][hapmap]
rs2300157	0.88[CHB][hapmap]
rs2300158	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2420015	0.89[CHB][hapmap]
rs2420016	0.89[CHB][hapmap]
rs3213586	0.89[CHB][hapmap]
rs3213587	0.88[CHB][hapmap]
rs3766090	0.88[CHB][hapmap]
rs3862937	0.89[CHB][hapmap]
rs3905328	0.81[YRI][hapmap]
rs4140538	0.88[CHB][hapmap]
rs4140539	0.88[CHB][hapmap]
rs6427185	0.81[YRI][hapmap]
rs6656822	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6697727	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700375	0.84[EUR][1000 genomes]
rs7524348	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs929133	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6672589	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs6672589	NME7	cis	Thyroid	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169429600-169434600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:169429600-169448200	Weak transcription	Fetal Heart	heart
3	chr1:169429800-169434400	Weak transcription	Placenta	Placenta
4	chr1:169429800-169436200	Weak transcription	Psoas Muscle	Psoas
5	chr1:169429800-169436200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:169429800-169436800	Weak transcription	Right Ventricle	heart
7	chr1:169429800-169446400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:169430000-169431200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:169430000-169434000	Weak transcription	HSMM	muscle
10	chr1:169430000-169434400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:169430000-169434600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:169430000-169434600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:169430000-169434600	Weak transcription	Left Ventricle	heart
14	chr1:169430000-169434600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:169430000-169434600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:169430000-169435000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:169430000-169435200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:169430000-169435200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:169430000-169436000	Weak transcription	Brain Anterior Caudate	brain
20	chr1:169430000-169436200	Weak transcription	Primary T cells from cord blood	blood
21	chr1:169430000-169436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:169430000-169436400	Weak transcription	Fetal Thymus	thymus
23	chr1:169430000-169443800	Weak transcription	Brain Substantia Nigra	brain
24	chr1:169430000-169444800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:169430000-169445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:169430000-169445600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:169430000-169446200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:169430000-169446200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:169430000-169446200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:169430000-169446400	Weak transcription	HUVEC	blood vessel
31	chr1:169430000-169450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
37	chr1:169430000-169452800	Weak transcription	HMEC	breast
38	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
39	chr1:169430000-169452800	Weak transcription	NHEK	skin
40	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
41	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
45	chr1:169430200-169431200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:169430200-169431200	Enhancers	Liver	Liver
47	chr1:169430200-169434200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:169430200-169434400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:169430200-169434600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:169430200-169434600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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