Variant report

Variant	rs16846094
Chromosome Location	chr1:224477652-224477653
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	chr1:224477255..224480181-chr1:224480396..224482235,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143748	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10158063	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10733024	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10737442	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737443	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799562	0.85[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799563	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799566	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799567	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799568	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916577	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802486	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11811730	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806742	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2001712	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001713	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2404783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404856	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404857	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404858	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404859	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405062	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2405065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405067	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405070	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2896990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896992	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897054	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767724	1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3767725	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233234	1.00[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]
rs4233235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4256779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4420060	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4457542	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4628473	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653575	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653583	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654011	0.88[ASN][1000 genomes]
rs4654017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654022	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654032	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654033	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654034	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55675086	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55980628	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57324770	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58855990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59106681	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426088	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6426094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6426110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426114	0.93[ASN][1000 genomes]
rs6426115	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426117	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685600	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6691689	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696795	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699017	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73118046	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73128468	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130436	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130448	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130455	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130462	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130464	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7522392	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7529143	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530205	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534101	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224424600-224479600	Weak transcription	Pancreas	Pancrea
2	chr1:224431200-224490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:224433400-224516200	Weak transcription	Fetal Heart	heart
4	chr1:224437000-224479600	Weak transcription	Right Ventricle	heart
5	chr1:224439800-224501600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:224444600-224479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:224445400-224482000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:224450800-224480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:224454800-224480000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:224455000-224480200	Weak transcription	Psoas Muscle	Psoas
11	chr1:224457200-224479600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:224461200-224505600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:224462200-224479600	Weak transcription	Spleen	Spleen
14	chr1:224465000-224487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:224465000-224488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:224465000-224504400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:224465000-224504400	Strong transcription	Liver	Liver
18	chr1:224465000-224505200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:224465000-224505600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:224465200-224487000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:224465400-224505600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:224465600-224477800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:224466200-224484200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:224466200-224487800	Strong transcription	NH-A	brain
25	chr1:224466400-224481200	Weak transcription	Small Intestine	intestine
26	chr1:224466400-224505400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:224466400-224505400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:224466400-224505600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:224466600-224505600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:224466800-224499200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:224467600-224484600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:224468000-224505200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:224468200-224496000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:224468600-224500000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:224469600-224478000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:224469800-224485600	Strong transcription	Fetal Intestine Large	intestine
37	chr1:224469800-224493200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:224470000-224477800	Strong transcription	HSMM	muscle
39	chr1:224470200-224480000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:224470400-224477800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:224471400-224479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:224471600-224480200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:224472200-224478000	Strong transcription	A549	lung
44	chr1:224472800-224478800	Weak transcription	HSMMtube	muscle
45	chr1:224473000-224496200	Strong transcription	Dnd41	blood
46	chr1:224473200-224477800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:224473200-224480200	Strong transcription	Placenta	Placenta
48	chr1:224473200-224497400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:224473600-224478000	Strong transcription	Fetal Lung	lung
50	chr1:224473600-224484000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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