Variant report

Variant	rs16846738
Chromosome Location	chr1:227142856-227142857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227130077..227134039-chr1:227140134..227143370,3	K562	blood:
2	chr1:227135011..227140362-chr1:227140387..227143822,8	K562	blood:
3	chr1:227141481..227143140-chr1:227143773..227146824,3	K562	blood:

Variant related genes	Relation type
ENSG00000228525	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12562621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12562646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12565025	1.00[ASN][1000 genomes]
rs12565212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12565685	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12567464	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12567790	0.92[ASN][1000 genomes]
rs12567972	0.88[ASN][1000 genomes]
rs12568014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1316851	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16841298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846716	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846731	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846733	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846735	0.85[ASN][1000 genomes]
rs16846751	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846779	0.92[ASN][1000 genomes]
rs16846780	0.92[ASN][1000 genomes]
rs16846783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846790	0.88[ASN][1000 genomes]
rs16846792	0.88[ASN][1000 genomes]
rs16846798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846808	0.92[ASN][1000 genomes]
rs16846811	0.92[ASN][1000 genomes]
rs16846903	1.00[JPT][hapmap]
rs16846944	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs16847001	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs16847020	0.86[CHB][hapmap]
rs2009053	0.92[ASN][1000 genomes]
rs2297411	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2297417	0.92[ASN][1000 genomes]
rs3738728	0.88[ASN][1000 genomes]
rs3795450	0.92[ASN][1000 genomes]
rs3795452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41527149	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4281295	0.92[ASN][1000 genomes]
rs4459073	0.92[ASN][1000 genomes]
rs4521963	0.92[ASN][1000 genomes]
rs56043893	0.92[ASN][1000 genomes]
rs60107850	1.00[ASN][1000 genomes]
rs944601	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs944602	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs961490	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv549268	chr1:227124660-227149203	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
7	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
2	chr1:227130200-227145600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:227130200-227146000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:227130400-227154600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:227131000-227171800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:227131400-227153800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:227131800-227147200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:227133000-227146200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:227133200-227149800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:227134400-227144800	Weak transcription	Fetal Intestine Large	intestine
11	chr1:227134400-227151800	Weak transcription	Small Intestine	intestine
12	chr1:227134400-227153000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:227134600-227150200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:227134800-227145000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:227134800-227149000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:227134800-227150200	Weak transcription	Brain Angular Gyrus	brain
17	chr1:227135000-227150600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:227135200-227149800	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:227135200-227152600	Weak transcription	Colonic Mucosa	Colon
20	chr1:227135200-227158000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:227135400-227146800	Weak transcription	Stomach Mucosa	stomach
22	chr1:227136200-227144800	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:227136200-227145200	Weak transcription	Brain Anterior Caudate	brain
24	chr1:227136200-227152800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:227136400-227146600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:227136400-227149200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:227137000-227146200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:227137400-227150400	Weak transcription	Aorta	Aorta
29	chr1:227137800-227146600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:227138000-227149000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:227138000-227152000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:227138400-227147800	Weak transcription	Primary T cells from cord blood	blood
33	chr1:227138800-227143000	Enhancers	Adipose Nuclei	Adipose
34	chr1:227139200-227151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:227139400-227149800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:227139400-227150600	Weak transcription	Primary B cells from cord blood	blood
37	chr1:227140000-227150200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:227140000-227152200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:227140000-227152800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:227140000-227153000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:227141200-227143000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
42	chr1:227141200-227143000	Strong transcription	HepG2	liver
43	chr1:227141200-227143200	Enhancers	Left Ventricle	heart
44	chr1:227141400-227149600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:227141600-227144800	Weak transcription	Psoas Muscle	Psoas
46	chr1:227141800-227145200	Weak transcription	Liver	Liver
47	chr1:227142000-227143000	Enhancers	Lung	lung
48	chr1:227142200-227143000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr1:227142200-227157800	Weak transcription	Fetal Lung	lung
50	chr1:227142400-227143000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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