Variant report

Variant	rs6703740
Chromosome Location	chr1:175041977-175041978
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175041206..175043201-chr1:175056003..175057829,2	K562	blood:
2	chr1:175041397..175042225-chr14:23298848..23299502,2	NB4	blood:

Variant related genes	Relation type
ENSG00000155465	Chromatin interaction
ENSG00000172590	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10912879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912882	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912883	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912884	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108523	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583029	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11586922	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070875	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12075389	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12087824	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12729551	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12737207	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12759791	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1573758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17374584	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17374654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894683	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1894684	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1894685	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1894686	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894687	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894688	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072030	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072031	0.84[JPT][hapmap]
rs2072032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072033	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2213851	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33944382	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35039562	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4471221	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4543755	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4618928	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4650697	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4651301	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425316	0.83[JPT][hapmap]
rs6425318	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425319	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425321	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6659648	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661403	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6681984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6683073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693368	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6694071	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696640	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs744008	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518405	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535254	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555464	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763249	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763250	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs763251	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs763252	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1011472	chr1:175013165-175042885	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1012861	chr1:175021780-175063160	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv535210	chr1:175021780-175063160	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv825487	chr1:175031609-175113572	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6703740	C1orf156	cis	parietal	SCAN
rs6703740	CACYBP	cis	cerebellum	SCAN
rs6703740	TNN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175039800-175042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:175039800-175046600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:175040400-175042800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:175040400-175043200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:175040600-175044000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:175040800-175042000	Enhancers	Fetal Lung	lung
7	chr1:175040800-175043000	Enhancers	Fetal Stomach	stomach
8	chr1:175041000-175042000	Enhancers	Lung	lung
9	chr1:175041000-175042200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:175041000-175042400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:175041000-175042400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:175041000-175042600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:175041000-175043000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:175041000-175043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:175041000-175043400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:175041000-175044000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:175041000-175044200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:175041000-175044200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:175041200-175042000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:175041200-175042000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:175041200-175042000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:175041200-175042000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:175041200-175042000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:175041200-175042000	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr1:175041200-175042200	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr1:175041200-175042200	Enhancers	Fetal Thymus	thymus
27	chr1:175041200-175042400	Enhancers	Placenta	Placenta
28	chr1:175041200-175042400	Enhancers	Spleen	Spleen
29	chr1:175041200-175042400	Flanking Active TSS	Dnd41	blood
30	chr1:175041200-175043200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr1:175041400-175042000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:175041400-175042000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:175041400-175042000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:175041400-175042000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:175041400-175042000	Active TSS	Brain Anterior Caudate	brain
36	chr1:175041400-175042000	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr1:175041400-175042000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:175041400-175042000	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:175041400-175042000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:175041400-175042200	Enhancers	Osteobl	bone
41	chr1:175041400-175042400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
42	chr1:175041400-175042400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr1:175041400-175042400	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr1:175041400-175042400	Enhancers	NHDF-Ad	bronchial
45	chr1:175041400-175042600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:175041400-175042800	Enhancers	GM12878-XiMat	blood
47	chr1:175041400-175043000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:175041400-175043000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr1:175041600-175042000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:175041600-175042000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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