Variant report

Variant	rs56835905
Chromosome Location	chr3:53073081-53073082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53072702..53076307-chr3:53077847..53082050,5	MCF-7	breast:
2	chr3:52964018..52964668-chr3:53072552..53073141,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs28696085	1.00[ASN][1000 genomes]
rs28719645	1.00[ASN][1000 genomes]
rs3806693	1.00[ASN][1000 genomes]
rs55794978	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55885034	1.00[ASN][1000 genomes]
rs56665986	0.91[AFR][1000 genomes]
rs56895623	0.92[AFR][1000 genomes]
rs57465047	0.85[AFR][1000 genomes]
rs57561909	0.85[AFR][1000 genomes]
rs57940327	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58249114	0.92[AFR][1000 genomes]
rs58309671	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58840385	1.00[ASN][1000 genomes]
rs58888768	0.85[AFR][1000 genomes]
rs59224641	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59515578	1.00[ASN][1000 genomes]
rs59838592	0.88[AFR][1000 genomes]
rs60648378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60744886	1.00[ASN][1000 genomes]
rs61285888	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61437303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61438885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6798309	0.91[AFR][1000 genomes]
rs6798669	0.92[AFR][1000 genomes]
rs72959478	0.80[AFR][1000 genomes]
rs72959499	0.80[AFR][1000 genomes]
rs72961724	0.85[AFR][1000 genomes]
rs72961730	0.85[AFR][1000 genomes]
rs72961733	0.85[AFR][1000 genomes]
rs72961742	0.91[AFR][1000 genomes]
rs72961752	0.91[AFR][1000 genomes]
rs72965340	0.92[AFR][1000 genomes]
rs72965345	1.00[ASN][1000 genomes]
rs72965348	0.92[AFR][1000 genomes]
rs72965350	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965354	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965358	0.89[AFR][1000 genomes]
rs72965359	0.92[AFR][1000 genomes]
rs72965361	1.00[ASN][1000 genomes]
rs72965362	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965370	0.88[AFR][1000 genomes]
rs72965381	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7618417	0.89[AFR][1000 genomes]
rs7628501	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7631487	1.00[ASN][1000 genomes]
rs9819608	1.00[ASN][1000 genomes]
rs9822686	1.00[ASN][1000 genomes]
rs9852646	1.00[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	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
2	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:53056600-53077800	Weak transcription	Fetal Stomach	stomach
4	chr3:53061800-53074400	Weak transcription	Osteobl	bone
5	chr3:53062200-53074400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:53062200-53076800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:53062200-53077000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:53064000-53078400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:53065400-53074400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:53065400-53077600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:53065400-53078600	Weak transcription	Gastric	stomach
12	chr3:53065600-53077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:53065800-53076200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:53066200-53076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:53068000-53077600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:53068600-53075000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:53068800-53077400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:53069200-53077800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:53069200-53077800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:53069800-53077600	Weak transcription	Stomach Mucosa	stomach
21	chr3:53070200-53077800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:53071000-53074400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:53071000-53076800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:53071000-53078400	Weak transcription	Right Ventricle	heart
25	chr3:53071000-53078600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:53071200-53074400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:53071200-53074600	Weak transcription	Fetal Heart	heart
28	chr3:53071200-53074600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:53071200-53076600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:53071400-53076200	Weak transcription	Dnd41	blood
31	chr3:53071400-53077800	Weak transcription	Left Ventricle	heart
32	chr3:53072000-53073200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:53072000-53074800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:53072000-53077000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:53072200-53074800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:53072200-53075600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr3:53072400-53074800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr3:53072400-53075000	Enhancers	Liver	Liver
39	chr3:53072600-53073400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:53072600-53073400	Enhancers	NHEK	skin
41	chr3:53072600-53073800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:53072600-53075000	Enhancers	HepG2	liver
43	chr3:53072800-53073400	Enhancers	HSMM	muscle
44	chr3:53072800-53073800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:53072800-53074600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr3:53072800-53075200	Enhancers	A549	lung
47	chr3:53072800-53075400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:53072800-53075400	Enhancers	HMEC	breast
49	chr3:53072800-53077800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:53073000-53073200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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