Variant report

Variant	rs2008604
Chromosome Location	chr21:46217378-46217379
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46213336..46214943-chr21:46217277..46219676,2	MCF-7	breast:
2	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
3	chr21:46216948..46220007-chr21:46331452..46334687,3	MCF-7	breast:
4	chr21:45926303..45927856-chr21:46215876..46218249,2	MCF-7	breast:
5	chr21:46204645..46207342-chr21:46215204..46218349,3	K562	blood:

Variant related genes	Relation type
ENSG00000160255	Chromatin interaction
ENSG00000235890	Chromatin interaction
ENSG00000183255	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12626275	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17004701	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17526563	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs235351	0.94[ASN][1000 genomes]
rs235362	0.94[ASN][1000 genomes]
rs235363	0.94[ASN][1000 genomes]
rs2838672	0.80[ASN][1000 genomes]
rs2838682	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838684	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838685	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838694	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838696	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35627976	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56357729	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7283211	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283639	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73232962	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73232966	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2008604	PTTG1IP	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
3	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr21:46198800-46219600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr21:46198800-46220000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:46198800-46220000	Weak transcription	Fetal Kidney	kidney
8	chr21:46200000-46220400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:46200400-46218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:46201200-46220400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:46202400-46219200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr21:46203400-46220000	Weak transcription	Fetal Brain Female	brain
13	chr21:46205200-46220400	Weak transcription	Aorta	Aorta
14	chr21:46205200-46220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr21:46206200-46218400	Weak transcription	Brain Anterior Caudate	brain
16	chr21:46206200-46219800	Weak transcription	Right Ventricle	heart
17	chr21:46206200-46220000	Weak transcription	Brain Germinal Matrix	brain
18	chr21:46206400-46220000	Weak transcription	Brain Hippocampus Middle	brain
19	chr21:46206800-46220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr21:46209800-46217800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr21:46210000-46220000	Weak transcription	Fetal Brain Male	brain
22	chr21:46210200-46220000	Weak transcription	NH-A	brain
23	chr21:46211600-46220400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr21:46211800-46220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr21:46212000-46220000	Weak transcription	Lung	lung
26	chr21:46212000-46220400	Weak transcription	Colonic Mucosa	Colon
27	chr21:46212400-46217600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr21:46212400-46220400	Weak transcription	Spleen	Spleen
29	chr21:46212600-46217800	Weak transcription	NHLF	lung
30	chr21:46212600-46219800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr21:46212800-46218000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr21:46213000-46218200	Weak transcription	Ovary	ovary
33	chr21:46213200-46217800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr21:46213400-46217800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr21:46213400-46217800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr21:46213400-46218800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr21:46213400-46219400	Weak transcription	Colon Smooth Muscle	Colon
38	chr21:46213400-46219400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr21:46213400-46219600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr21:46213400-46219600	Weak transcription	Psoas Muscle	Psoas
41	chr21:46213400-46219800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr21:46213400-46219800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr21:46213400-46219800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr21:46213400-46219800	Weak transcription	Brain Substantia Nigra	brain
45	chr21:46213400-46219800	Weak transcription	Fetal Heart	heart
46	chr21:46213400-46219800	Weak transcription	Pancreas	Pancrea
47	chr21:46213400-46219800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr21:46213400-46219800	Weak transcription	HSMMtube	muscle
49	chr21:46213400-46220000	Weak transcription	Esophagus	oesophagus
50	chr21:46213400-46220000	Weak transcription	Right Atrium	heart

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