Variant report

Variant	rs35528262
Chromosome Location	chr2:73955125-73955126
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73954066..73956165-chr2:73960513..73963434,2	MCF-7	breast:
2	chr2:73954874..73956746-chr2:74424567..74426478,2	MCF-7	breast:
3	chr2:73943613..73945709-chr2:73953816..73955383,2	MCF-7	breast:
4	chr2:73954918..73956793-chr2:73957164..73959420,2	MCF-7	breast:
5	chr2:73945415..73947505-chr2:73953398..73955264,2	K562	blood:

Variant related genes	Relation type
ENSG00000144034	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10191988	0.83[EUR][1000 genomes]
rs11891140	0.82[EUR][1000 genomes]
rs11894953	0.82[EUR][1000 genomes]
rs12615807	0.83[EUR][1000 genomes]
rs12713789	0.82[EUR][1000 genomes]
rs12713790	0.82[EUR][1000 genomes]
rs12713791	0.82[EUR][1000 genomes]
rs12713793	0.83[EUR][1000 genomes]
rs12713794	0.82[EUR][1000 genomes]
rs12713795	0.82[EUR][1000 genomes]
rs12713797	0.80[EUR][1000 genomes]
rs12992607	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13003035	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17350188	0.82[EUR][1000 genomes]
rs1806683	0.80[EUR][1000 genomes]
rs1815028	0.80[EUR][1000 genomes]
rs2006997	0.83[EUR][1000 genomes]
rs2421557	0.80[EUR][1000 genomes]
rs2421672	0.83[EUR][1000 genomes]
rs2421674	0.83[EUR][1000 genomes]
rs2421675	0.83[EUR][1000 genomes]
rs2421676	0.81[EUR][1000 genomes]
rs3980695	0.80[EUR][1000 genomes]
rs4241257	0.80[EUR][1000 genomes]
rs4358149	0.83[EUR][1000 genomes]
rs4852977	0.80[EUR][1000 genomes]
rs4852978	0.82[EUR][1000 genomes]
rs6748233	0.80[EUR][1000 genomes]
rs6749841	0.82[EUR][1000 genomes]
rs6750494	0.82[EUR][1000 genomes]
rs6750515	0.82[EUR][1000 genomes]
rs6755500	0.82[EUR][1000 genomes]
rs7210	0.83[EUR][1000 genomes]
rs7591112	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv2753082	chr2:73891045-73955545	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	nsv998315	chr2:73919185-74003998	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS 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	11 gene(s)	inside rSNPs	diseases
9	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
10	nsv1003153	chr2:73927235-73975416	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35528262	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs35528262	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs35528262	ALMS1P	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73935000-73955200	Weak transcription	Colonic Mucosa	Colon
2	chr2:73944000-73958000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:73944200-73955400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:73944400-73955400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:73944400-73958000	Weak transcription	Osteobl	bone
6	chr2:73944600-73963000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:73944600-73963600	Weak transcription	Stomach Mucosa	stomach
8	chr2:73947800-73955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:73950000-73955400	Weak transcription	Aorta	Aorta
10	chr2:73951000-73955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:73951600-73957600	Weak transcription	K562	blood
12	chr2:73952200-73958000	Weak transcription	HUVEC	blood vessel
13	chr2:73952200-73958400	Weak transcription	NHDF-Ad	bronchial
14	chr2:73952400-73955600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:73952600-73955800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:73952800-73955200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:73952800-73955400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:73952800-73955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:73953200-73955200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:73953200-73955200	Weak transcription	Placenta	Placenta
21	chr2:73953200-73955400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:73953200-73957200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:73953200-73957400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:73953200-73957800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:73953200-73959400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:73953200-73963600	Weak transcription	Small Intestine	intestine
27	chr2:73953400-73955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:73953400-73955200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:73953400-73955200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:73953400-73955200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:73953400-73957000	Weak transcription	Hela-S3	cervix
32	chr2:73953400-73958000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:73953400-73958000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:73953400-73958000	Weak transcription	NHLF	lung
35	chr2:73953600-73955200	Weak transcription	Fetal Thymus	thymus
36	chr2:73953600-73955200	Weak transcription	Left Ventricle	heart
37	chr2:73953600-73955400	Weak transcription	Brain Substantia Nigra	brain
38	chr2:73953600-73955400	Weak transcription	Gastric	stomach
39	chr2:73953600-73955400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:73953600-73956000	Weak transcription	HMEC	breast
41	chr2:73953600-73957800	Weak transcription	Fetal Lung	lung
42	chr2:73953800-73955600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:73953800-73957200	Weak transcription	NH-A	brain
44	chr2:73953800-73957600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:73954000-73955600	Weak transcription	Right Ventricle	heart
46	chr2:73954000-73963000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:73954200-73955800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:73954200-73957600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:73954200-73958000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:73954200-73958200	Weak transcription	Psoas Muscle	Psoas

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