Variant report

Variant	rs2567601
Chromosome Location	chr2:73985167-73985168
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:73985032..73987699-chr2:74002140..74003888,2	K562	blood:
2	chr2:73983484..73986212-chr2:74007345..74009528,2	K562	blood:
3	chr2:73983484..73986355-chr2:74005488..74009528,4	K562	blood:
4	chr2:73985050..73987926-chr2:73998150..74000912,3	MCF-7	breast:
5	chr2:73983418..73985845-chr2:73988941..73990622,2	K562	blood:
6	chr2:73983418..73985987-chr2:73988292..73990441,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf78-3	chr2:73982148-73988270	NONHSAT071632

No data

Variant related genes	Relation type
ENSG00000144048	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10168931	1.00[ASN][1000 genomes]
rs10169213	1.00[ASN][1000 genomes]
rs10169714	1.00[ASN][1000 genomes]
rs10173534	1.00[ASN][1000 genomes]
rs10181563	1.00[ASN][1000 genomes]
rs10185080	1.00[ASN][1000 genomes]
rs10188058	1.00[JPT][hapmap]
rs10197755	1.00[ASN][1000 genomes]
rs10198549	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10207220	1.00[ASN][1000 genomes]
rs1025424	1.00[JPT][hapmap]
rs1114380	1.00[ASN][1000 genomes]
rs11675958	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689164	1.00[ASN][1000 genomes]
rs11689234	0.80[CEU][hapmap]
rs11893881	1.00[ASN][1000 genomes]
rs1318987	1.00[JPT][hapmap]
rs13384756	1.00[ASN][1000 genomes]
rs13391552	1.00[ASN][1000 genomes]
rs13409366	1.00[ASN][1000 genomes]
rs13410232	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13431529	1.00[ASN][1000 genomes]
rs13432605	1.00[ASN][1000 genomes]
rs13538	1.00[ASN][1000 genomes]
rs17009149	1.00[ASN][1000 genomes]
rs17009159	1.00[ASN][1000 genomes]
rs17725971	1.00[JPT][hapmap]
rs2567598	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2567602	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567603	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	1.00[ASN][1000 genomes]
rs4547554	1.00[ASN][1000 genomes]
rs62149774	1.00[ASN][1000 genomes]
rs62149777	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[JPT][hapmap];1.00[ASN][1000 genomes]
rs6710438	1.00[ASN][1000 genomes]
rs6735946	1.00[ASN][1000 genomes]
rs6744398	1.00[ASN][1000 genomes]
rs6745368	1.00[ASN][1000 genomes]
rs6756885	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6759452	0.83[CEU][hapmap];1.00[JPT][hapmap];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]
rs7583255	1.00[ASN][1000 genomes]
rs7586463	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]
rs9653557	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	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
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2567601	ALMS1P	cis	Thyroid	GTEx
rs2567601	ALMS1P	cis	Nerve Tibial	GTEx
rs2567601	ALMS1	cis	normal skin	skin_eQTL
rs2567601	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2567601	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr2:73965000-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:73965400-73985600	Weak transcription	Fetal Heart	heart
4	chr2:73965400-73986200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:73965400-73986600	Weak transcription	Psoas Muscle	Psoas
6	chr2:73966200-73992000	Weak transcription	Stomach Mucosa	stomach
7	chr2:73969400-73987200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:73969600-73986000	Weak transcription	Right Ventricle	heart
9	chr2:73971400-74002200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:73971600-73987000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:73972000-73992200	Weak transcription	Fetal Kidney	kidney
12	chr2:73973400-73987400	Weak transcription	Colonic Mucosa	Colon
13	chr2:73974000-73986000	Weak transcription	Small Intestine	intestine
14	chr2:73974000-73989000	Weak transcription	Fetal Brain Male	brain
15	chr2:73974200-73986800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:73974400-73987000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:73974600-73985800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:73976400-73986200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:73976600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:73977200-73995000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:73977400-73985600	Strong transcription	Adipose Nuclei	Adipose
22	chr2:73977400-73986000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:73977400-73986400	Strong transcription	Fetal Muscle Leg	muscle
24	chr2:73977400-73993000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:73977400-74001400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:73977400-74004800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:73977600-74004800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:73977800-74004000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:73978000-74004200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:73978200-73998400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:73978800-73995200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:73980000-73987200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:73980000-73988800	Weak transcription	K562	blood
34	chr2:73980200-73986600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:73980600-73986000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:73980600-73986800	Weak transcription	Brain Angular Gyrus	brain
37	chr2:73980800-73986000	Weak transcription	NHDF-Ad	bronchial
38	chr2:73980800-73986600	Weak transcription	HSMMtube	muscle
39	chr2:73980800-73991400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:73981400-73994000	Strong transcription	Thymus	Thymus
41	chr2:73981600-73986200	Strong transcription	Lung	lung
42	chr2:73981600-74004800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:73981800-73985400	Strong transcription	Fetal Thymus	thymus
44	chr2:73981800-73986000	Strong transcription	Fetal Intestine Small	intestine
45	chr2:73981800-73986600	Strong transcription	NH-A	brain
46	chr2:73981800-73986800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:73981800-73994000	Strong transcription	Fetal Stomach	stomach
48	chr2:73982000-73985400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:73982000-73985800	Strong transcription	GM12878-XiMat	blood
50	chr2:73982000-74004600	Strong transcription	Primary T cells from cord blood	blood

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