Variant report

Variant	rs2567598
Chromosome Location	chr2:74004071-74004072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73991479..73993446-chr2:74004055..74006417,2	MCF-7	breast:
2	chr2:73998796..74000757-chr2:74002407..74004456,2	MCF-7	breast:
3	chr2:74003041..74008140-chr2:74055591..74058388,4	MCF-7	breast:
4	chr2:73985324..73987397-chr2:74002971..74004836,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124356	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10168931	1.00[ASN][1000 genomes]
rs10169714	1.00[ASN][1000 genomes]
rs10173534	1.00[ASN][1000 genomes]
rs1114380	1.00[ASN][1000 genomes]
rs11675958	1.00[ASN][1000 genomes]
rs11689164	1.00[ASN][1000 genomes]
rs11893881	1.00[ASN][1000 genomes]
rs13384756	1.00[ASN][1000 genomes]
rs13391552	1.00[ASN][1000 genomes]
rs13409366	1.00[ASN][1000 genomes]
rs13410232	1.00[ASN][1000 genomes]
rs13431529	1.00[ASN][1000 genomes]
rs13432605	1.00[ASN][1000 genomes]
rs13538	1.00[ASN][1000 genomes]
rs2567600	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2567601	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567602	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567603	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	1.00[ASN][1000 genomes]
rs4547554	1.00[ASN][1000 genomes]
rs62149781	1.00[ASN][1000 genomes]
rs62149782	1.00[ASN][1000 genomes]
rs62149804	1.00[ASN][1000 genomes]
rs6546854	1.00[ASN][1000 genomes]
rs6546857	1.00[ASN][1000 genomes]
rs6710438	1.00[ASN][1000 genomes]
rs6744398	1.00[ASN][1000 genomes]
rs6745368	1.00[ASN][1000 genomes]
rs6756885	1.00[ASN][1000 genomes]
rs6759452	1.00[ASN][1000 genomes]
rs7424690	1.00[ASN][1000 genomes]
rs7558944	1.00[ASN][1000 genomes]
rs7582051	1.00[ASN][1000 genomes]
rs7582606	1.00[ASN][1000 genomes]
rs7587577	1.00[ASN][1000 genomes]
rs7596773	1.00[ASN][1000 genomes]
rs7603647	1.00[ASN][1000 genomes]
rs7607892	1.00[ASN][1000 genomes]
rs9750915	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	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
6	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2567598	ALMS1P	cis	Thyroid	GTEx
rs2567598	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2567598	ALMS1P	cis	Nerve Tibial	GTEx
rs2567598	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73964600-74005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:73976600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:73977400-74004800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr2:73977600-74004800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:73978000-74004200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:73981600-74004800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr2:73982000-74004600	Strong transcription	Primary T cells from cord blood	blood
8	chr2:73982000-74004800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr2:73982000-74005200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:73982200-74004800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:73982200-74005200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:73982400-74004800	Strong transcription	Placenta	Placenta
13	chr2:73982400-74005000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:73982600-74005000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:73982600-74005000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:73982800-74004800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:73982800-74005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:73983000-74005000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:73983400-74004400	Strong transcription	HepG2	liver
20	chr2:73983600-74005400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:73983600-74006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:73983800-74006000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:73986200-74005200	Strong transcription	Fetal Thymus	thymus
24	chr2:73987000-74004400	Strong transcription	Hela-S3	cervix
25	chr2:73987000-74005200	Strong transcription	Fetal Muscle Leg	muscle
26	chr2:73987200-74005000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:73987200-74005400	Weak transcription	Psoas Muscle	Psoas
28	chr2:73987400-74005000	Strong transcription	Liver	Liver
29	chr2:73987600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:73987600-74004400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:73987600-74004600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:73988200-74005400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:73988200-74005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:73991000-74004800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:73992600-74006000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:73992800-74005600	Weak transcription	Stomach Mucosa	stomach
37	chr2:73993400-74006200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:73993800-74005400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:73994000-74005600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:73995600-74006000	Weak transcription	Right Ventricle	heart
41	chr2:73995600-74006200	Weak transcription	Aorta	Aorta
42	chr2:73995600-74006600	Weak transcription	Spleen	Spleen
43	chr2:73996000-74006600	Weak transcription	Gastric	stomach
44	chr2:73997000-74005600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:73997800-74004800	Strong transcription	HUVEC	blood vessel
46	chr2:73998000-74004200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:73998600-74005600	Weak transcription	Lung	lung
48	chr2:73999200-74004400	Strong transcription	Brain Germinal Matrix	brain
49	chr2:73999200-74004600	Strong transcription	Brain Substantia Nigra	brain
50	chr2:73999200-74005000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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