Variant report

Variant	rs16846783
Chromosome Location	chr1:227188616-227188617
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227173653..227176046-chr1:227186826..227189560,2	MCF-7	breast:
2	chr1:227176058..227178515-chr1:227186795..227190068,3	MCF-7	breast:
3	chr1:227182754..227185276-chr1:227188097..227190742,3	K562	blood:
4	chr1:227178460..227180582-chr1:227186986..227189766,2	K562	blood:

Variant related genes	Relation type
ENSG00000233706	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12562621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12562646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12565025	0.92[ASN][1000 genomes]
rs12565212	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12565685	0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12567464	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs12567790	1.00[ASN][1000 genomes]
rs12567972	0.96[ASN][1000 genomes]
rs12568014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12569190	0.84[ASN][1000 genomes]
rs12569194	0.84[ASN][1000 genomes]
rs1316851	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16841298	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846716	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846731	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846733	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846779	1.00[ASN][1000 genomes]
rs16846780	1.00[ASN][1000 genomes]
rs16846790	0.96[ASN][1000 genomes]
rs16846792	0.96[ASN][1000 genomes]
rs16846798	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846808	1.00[ASN][1000 genomes]
rs16846811	1.00[ASN][1000 genomes]
rs16846862	0.84[ASN][1000 genomes]
rs16846867	0.84[ASN][1000 genomes]
rs16846903	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16846944	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16847001	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16847020	0.89[CHB][hapmap]
rs16847137	0.84[ASN][1000 genomes]
rs2009053	0.84[ASN][1000 genomes]
rs2297411	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2297417	1.00[ASN][1000 genomes]
rs3738728	0.96[ASN][1000 genomes]
rs3795450	1.00[ASN][1000 genomes]
rs3795452	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41527149	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4281295	0.84[ASN][1000 genomes]
rs4459073	0.84[ASN][1000 genomes]
rs4521963	0.84[ASN][1000 genomes]
rs56043893	1.00[ASN][1000 genomes]
rs60107850	0.92[ASN][1000 genomes]
rs944601	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs944602	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs961490	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:227175200-227198400	Weak transcription	A549	lung
4	chr1:227175200-227210200	Weak transcription	HMEC	breast
5	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
7	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:227176000-227216400	Weak transcription	NHLF	lung
9	chr1:227176400-227190400	Weak transcription	Osteobl	bone
10	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
12	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
14	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:227178800-227188800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
19	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
20	chr1:227179600-227213800	Weak transcription	NH-A	brain
21	chr1:227180800-227190200	Weak transcription	K562	blood
22	chr1:227181200-227190400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:227181600-227191200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:227182000-227190200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:227182200-227190200	Weak transcription	Ovary	ovary
27	chr1:227182200-227205600	Weak transcription	Fetal Brain Male	brain
28	chr1:227182400-227190800	Weak transcription	NHEK	skin
29	chr1:227182600-227189000	Weak transcription	Fetal Brain Female	brain
30	chr1:227182600-227190000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:227182600-227190200	Weak transcription	Gastric	stomach
32	chr1:227182600-227190200	Weak transcription	Right Ventricle	heart
33	chr1:227182600-227191400	Weak transcription	Fetal Kidney	kidney
34	chr1:227182600-227206400	Weak transcription	Brain Germinal Matrix	brain
35	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
36	chr1:227183000-227190200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:227183000-227190400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:227183000-227191000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:227183200-227188800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:227183200-227190200	Weak transcription	Brain Angular Gyrus	brain
41	chr1:227183200-227202600	Weak transcription	Pancreas	Pancrea
42	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
44	chr1:227183600-227204600	Weak transcription	HepG2	liver
45	chr1:227183800-227188800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:227183800-227189000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:227183800-227203000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:227184000-227190400	Weak transcription	Fetal Heart	heart
49	chr1:227184000-227191000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:227184000-227203200	Weak transcription	Brain Substantia Nigra	brain

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