Variant report

Variant	rs55909105
Chromosome Location	chr6:88394850-88394851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88370220..88371861-chr6:88394700..88396720,2	K562	blood:
2	chr6:88391233..88396986-chr6:88407673..88412388,9	K562	blood:
3	chr6:88391827..88396132-chr6:88405533..88410317,6	MCF-7	breast:
4	chr6:88388879..88390685-chr6:88392735..88395490,2	MCF-7	breast:
5	chr6:88394474..88397021-chr6:88403318..88405135,2	K562	blood:
6	chr6:88388778..88396986-chr6:88407117..88413072,10	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs16879704	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28381530	0.91[ASN][1000 genomes]
rs3763177	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs41273297	0.83[ASN][1000 genomes]
rs55985738	0.83[ASN][1000 genomes]
rs56400749	0.83[ASN][1000 genomes]
rs57573658	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58060521	0.87[AFR][1000 genomes]
rs59774543	0.83[ASN][1000 genomes]
rs60082015	0.83[ASN][1000 genomes]
rs60316099	0.83[ASN][1000 genomes]
rs66502414	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs66965134	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67993159	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs68082038	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6907107	0.83[ASN][1000 genomes]
rs715207	0.88[ASN][1000 genomes]
rs72924341	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72924342	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73498106	0.83[ASN][1000 genomes]
rs7747792	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7752473	0.83[ASN][1000 genomes]
rs7769144	0.83[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	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
5	chr6:88349400-88397400	Weak transcription	Ovary	ovary
6	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
8	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
9	chr6:88385400-88399800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:88385400-88401200	Weak transcription	Fetal Heart	heart
11	chr6:88385800-88398600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:88385800-88399200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:88386000-88396400	Weak transcription	Lung	lung
14	chr6:88386200-88399000	Weak transcription	Gastric	stomach
15	chr6:88387400-88398600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:88387600-88397000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
18	chr6:88387800-88400600	Weak transcription	K562	blood
19	chr6:88388000-88397200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:88388000-88401400	Weak transcription	Placenta	Placenta
21	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
23	chr6:88389400-88396400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:88389600-88401400	Weak transcription	Fetal Brain Female	brain
25	chr6:88390200-88401200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr6:88390400-88396000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:88390400-88398800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:88390400-88399600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:88390400-88400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:88390400-88400800	Weak transcription	Pancreas	Pancrea
31	chr6:88390400-88401200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:88390400-88401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:88390400-88401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:88391200-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:88391400-88395000	Weak transcription	Brain Angular Gyrus	brain
39	chr6:88391400-88395400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:88391400-88400800	Weak transcription	Brain Germinal Matrix	brain
41	chr6:88391400-88400800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:88391600-88395800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:88391600-88395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:88391600-88399400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:88391800-88395400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr6:88391800-88395600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:88391800-88395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:88391800-88396200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:88391800-88396200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:88391800-88399600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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