Variant report

Variant	rs16846716
Chromosome Location	chr1:227133011-227133012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227129578..227135154-chr1:227160579..227165321,6	K562	blood:
2	chr1:227130077..227134039-chr1:227140134..227143370,3	K562	blood:
3	chr1:227129122..227132019-chr1:227132430..227134226,2	MCF-7	breast:
4	chr1:227131547..227134077-chr1:227151435..227154330,2	K562	blood:
5	chr1:227131339..227134791-chr1:227138327..227140001,4	MCF-7	breast:
6	chr1:227126597..227128244-chr1:227132105..227134176,2	MCF-7	breast:
7	chr1:227132668..227135154-chr1:227162746..227165321,2	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12562621	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs12562646	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs12564719	1.00[GIH][hapmap]
rs12565025	0.92[ASN][1000 genomes]
rs12565212	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs12567464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12567790	0.84[ASN][1000 genomes]
rs12567972	0.81[ASN][1000 genomes]
rs12568014	0.84[ASN][1000 genomes]
rs1316851	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16841298	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs16846733	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846735	0.92[ASN][1000 genomes]
rs16846738	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846751	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846772	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846779	0.84[ASN][1000 genomes]
rs16846780	0.84[ASN][1000 genomes]
rs16846783	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846790	0.81[ASN][1000 genomes]
rs16846792	0.81[ASN][1000 genomes]
rs16846798	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846808	0.84[ASN][1000 genomes]
rs16846811	0.84[ASN][1000 genomes]
rs2009053	1.00[ASN][1000 genomes]
rs2297411	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs2297417	0.84[ASN][1000 genomes]
rs3738728	0.81[ASN][1000 genomes]
rs3795450	0.84[ASN][1000 genomes]
rs3795452	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs41527149	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs4281295	1.00[ASN][1000 genomes]
rs4459073	1.00[ASN][1000 genomes]
rs4521963	1.00[ASN][1000 genomes]
rs56043893	0.84[ASN][1000 genomes]
rs60107850	0.92[ASN][1000 genomes]
rs944601	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs944602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227128600-227136600	Weak transcription	Aorta	Aorta
2	chr1:227128800-227135400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr1:227129000-227133400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:227129000-227133600	Enhancers	Spleen	Spleen
5	chr1:227129000-227134400	Enhancers	Fetal Intestine Large	intestine
6	chr1:227129000-227134400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr1:227129000-227134400	Weak transcription	NHDF-Ad	bronchial
8	chr1:227129000-227134800	Weak transcription	Fetal Brain Female	brain
9	chr1:227129000-227135000	Enhancers	Fetal Muscle Leg	muscle
10	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
11	chr1:227129200-227133200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:227129200-227133400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:227129200-227133400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:227129200-227133400	Enhancers	K562	blood
15	chr1:227129200-227133800	Enhancers	Brain Angular Gyrus	brain
16	chr1:227129200-227134000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:227129200-227134800	Enhancers	Brain Anterior Caudate	brain
18	chr1:227129200-227134800	Enhancers	Brain Hippocampus Middle	brain
19	chr1:227129200-227134800	Enhancers	Brain Substantia Nigra	brain
20	chr1:227129200-227134800	Enhancers	Gastric	stomach
21	chr1:227129200-227135000	Enhancers	Fetal Heart	heart
22	chr1:227129200-227135000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:227129200-227135200	Enhancers	Colon Smooth Muscle	Colon
24	chr1:227129200-227135400	Enhancers	Stomach Mucosa	stomach
25	chr1:227129200-227135800	Weak transcription	Fetal Stomach	stomach
26	chr1:227129400-227133400	Weak transcription	Fetal Brain Male	brain
27	chr1:227129600-227134600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:227130000-227133800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:227130000-227133800	Weak transcription	Placenta	Placenta
30	chr1:227130000-227134200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:227130200-227134800	Enhancers	Fetal Intestine Small	intestine
32	chr1:227130200-227134800	Enhancers	Ovary	ovary
33	chr1:227130200-227145600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:227130200-227146000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:227130400-227133200	Enhancers	Adipose Nuclei	Adipose
36	chr1:227130400-227134600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:227130400-227134800	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:227130400-227137000	Weak transcription	Primary B cells from cord blood	blood
39	chr1:227130400-227137000	Weak transcription	Primary T cells from cord blood	blood
40	chr1:227130400-227141000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:227130400-227142400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:227130400-227142400	Weak transcription	Hela-S3	cervix
43	chr1:227130400-227154600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:227130800-227133400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:227130800-227142400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:227131000-227134400	Flanking Active TSS	HepG2	liver
47	chr1:227131000-227171800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:227131400-227133400	Enhancers	Colonic Mucosa	Colon
49	chr1:227131400-227134400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr1:227131400-227153800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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