Variant report

Variant	rs16848029
Chromosome Location	chr1:227845283-227845284
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227840840..227843527-chr1:227844086..227846913,2	K562	blood:
2	chr1:227840840..227843774-chr1:227844086..227846968,3	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10047205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1021553	0.87[JPT][hapmap]
rs1021554	0.82[JPT][hapmap]
rs10799432	0.87[JPT][hapmap]
rs10799435	0.87[JPT][hapmap]
rs10916165	0.87[JPT][hapmap]
rs10916178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916182	0.91[JPT][hapmap]
rs10916187	0.83[JPT][hapmap]
rs10916192	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025815	0.91[JPT][hapmap]
rs12059899	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12069550	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12070002	0.91[JPT][hapmap]
rs12070036	0.91[JPT][hapmap]
rs12070539	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080321	0.87[JPT][hapmap]
rs12080590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12082414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12092295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12095502	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12096675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132444	0.87[JPT][hapmap]
rs1407718	0.83[JPT][hapmap]
rs1495846	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1495849	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16847966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16847991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16847992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1923821	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012432	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2093609	0.87[JPT][hapmap]
rs2132366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132367	0.91[JPT][hapmap]
rs2256599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2453682	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2644143	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2644144	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644146	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644153	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2644161	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814059	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2814060	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2814061	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814084	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2814085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2819496	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2819498	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2819507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2819511	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2935146	0.87[JPT][hapmap]
rs2935152	0.86[JPT][hapmap]
rs2935155	0.91[JPT][hapmap]
rs2999745	0.91[JPT][hapmap]
rs2999746	0.87[JPT][hapmap]
rs3010183	0.86[JPT][hapmap]
rs3010186	0.91[JPT][hapmap]
rs3010190	0.82[JPT][hapmap]
rs3010191	0.86[JPT][hapmap]
rs3010192	0.91[JPT][hapmap]
rs3010193	0.91[JPT][hapmap]
rs3010194	0.83[JPT][hapmap]
rs3748806	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4376731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4589104	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653514	0.87[JPT][hapmap]
rs4653849	0.86[JPT][hapmap]
rs4653853	0.83[JPT][hapmap]
rs58020705	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59034043	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59149651	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59753688	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61343450	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66471275	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66491073	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659745	0.84[EUR][1000 genomes]
rs66736638	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683151	0.91[JPT][hapmap]
rs6688145	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693348	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66938123	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6697867	0.83[JPT][hapmap]
rs67216605	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67511833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67676707	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68046179	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68186506	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72632830	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72632831	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72632832	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72748074	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7413796	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7528094	0.86[JPT][hapmap]
rs753541	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903690	0.86[JPT][hapmap]
rs903692	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903693	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903694	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903695	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs965942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16848029	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs16848029	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
4	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
9	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr1:227832600-227846400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr1:227834000-227847200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:227835000-227852200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:227835000-227852600	ZNF genes & repeats	Fetal Brain Female	brain
18	chr1:227835200-227847800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
19	chr1:227836400-227852200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr1:227838400-227846600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:227838600-227845400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:227838600-227845400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
23	chr1:227838600-227847200	ZNF genes & repeats	Brain Substantia Nigra	brain
24	chr1:227838600-227849800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:227838600-227854400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:227838800-227849800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
27	chr1:227839600-227847000	Weak transcription	Pancreas	Pancrea
28	chr1:227840600-227845400	ZNF genes & repeats	Fetal Lung	lung
29	chr1:227841200-227852000	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr1:227841200-227852600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr1:227841200-227852800	ZNF genes & repeats	Brain Anterior Caudate	brain
32	chr1:227841400-227846400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:227841600-227852600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
34	chr1:227842000-227846400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
35	chr1:227842800-227845800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:227843000-227846000	Weak transcription	Aorta	Aorta
37	chr1:227843200-227849400	Weak transcription	Fetal Thymus	thymus
38	chr1:227843200-227851200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:227844200-227847400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:227844400-227846200	ZNF genes & repeats	Fetal Brain Male	brain
41	chr1:227844400-227846400	ZNF genes & repeats	HSMM	muscle
42	chr1:227844400-227847400	ZNF genes & repeats	Brain Hippocampus Middle	brain
43	chr1:227844600-227845400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:227844600-227846400	Active TSS	Right Atrium	heart
45	chr1:227844600-227850800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:227845000-227847000	Weak transcription	Placenta	Placenta
47	chr1:227845200-227846200	Weak transcription	Left Ventricle	heart
48	chr1:227845200-227846200	Weak transcription	Ovary	ovary

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