Variant report

Variant	rs2421676
Chromosome Location	chr2:73966087-73966088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73964465..73966386-chr2:74680896..74683797,3	MCF-7	breast:
2	chr2:73956564..73959101-chr2:73964667..73967117,2	MCF-7	breast:
3	chr2:73964502..73966089-chr2:74005861..74007990,2	MCF-7	breast:
4	chr2:73964687..73966201-chr2:73967226..73969278,2	K562	blood:
5	chr2:73963713..73965775-chr2:73965879..73968713,3	K562	blood:

Variant related genes	Relation type
ENSG00000144034	Chromatin interaction
ENSG00000115274	Chromatin interaction
ENSG00000144048	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10172044	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10190002	0.81[TSI][hapmap]
rs10191988	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10193032	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs10200762	0.81[AMR][1000 genomes]
rs10203740	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10208995	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1052161	0.81[TSI][hapmap]
rs11126414	0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11126415	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11126416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11126417	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11891140	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11892172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11894953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052539	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12053242	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12233112	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs12233115	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12611487	0.83[EUR][1000 genomes]
rs12612423	0.83[EUR][1000 genomes]
rs12615807	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12618600	0.83[TSI][hapmap]
rs12619258	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12624267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713788	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12713789	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12713790	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12713791	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12713793	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713794	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713795	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713797	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12992607	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12997568	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12998980	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs13000788	0.83[EUR][1000 genomes]
rs13003035	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13005729	0.85[EUR][1000 genomes]
rs13006448	0.85[EUR][1000 genomes]
rs13006598	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13013228	0.85[EUR][1000 genomes]
rs13014700	0.84[EUR][1000 genomes]
rs13015885	0.84[EUR][1000 genomes]
rs13017182	0.84[GIH][hapmap]
rs13020517	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13031853	0.85[EUR][1000 genomes]
rs13031866	0.85[EUR][1000 genomes]
rs13033744	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320374	0.81[TSI][hapmap]
rs13383097	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17350056	0.85[EUR][1000 genomes]
rs17350125	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17350188	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17434634	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17434655	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1806683	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1815028	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001436	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2001490	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2006997	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2012574	0.85[EUR][1000 genomes]
rs2116367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272051	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2272178	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421557	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421558	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421559	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421574	0.92[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs2421575	0.84[EUR][1000 genomes]
rs2421586	0.83[TSI][hapmap]
rs2421668	0.83[TSI][hapmap]
rs2421672	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421674	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421675	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2421677	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2462127	0.88[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35498419	0.92[EUR][1000 genomes]
rs35528262	0.81[EUR][1000 genomes]
rs35767294	0.85[EUR][1000 genomes]
rs35791379	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813228	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3980695	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4241257	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4358149	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4513320	0.85[EUR][1000 genomes]
rs4530394	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4852316	0.90[EUR][1000 genomes]
rs4852972	0.83[EUR][1000 genomes]
rs4852975	0.87[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4852976	0.91[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4852977	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4852978	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6732812	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6745560	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs6748233	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6749841	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6750494	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6750515	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6750877	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6755500	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7210	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs732778	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7370393	0.85[EUR][1000 genomes]
rs7558546	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7570683	0.83[TSI][hapmap]
rs7591112	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7597302	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7599453	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7606947	0.92[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs891695	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs891696	0.90[EUR][1000 genomes]
rs9309475	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9309476	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2421676	ALMS1	cis	parietal	SCAN
rs2421676	ALMS1	cis	cerebellum	SCAN
rs2421676	ALMS1P	cis	Nerve Tibial	GTEx
rs2421676	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2421676	DUSP11	cis	cerebellum	SCAN
rs2421676	ALMS1P	cis	parietal	SCAN
rs2421676	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2421676	DUSP11	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73964400-73973200	Weak transcription	Small Intestine	intestine
2	chr2:73964600-74005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:73964800-73973200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:73964800-73973400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:73965000-73966400	Weak transcription	Esophagus	oesophagus
6	chr2:73965000-73966600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:73965000-73968400	Weak transcription	Aorta	Aorta
8	chr2:73965000-73968600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:73965000-73968600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:73965000-73968600	Weak transcription	Ovary	ovary
11	chr2:73965000-73968800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:73965000-73968800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:73965000-73971400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:73965000-73971800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:73965000-73973000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:73965000-73973000	Weak transcription	Colonic Mucosa	Colon
17	chr2:73965000-73973000	Weak transcription	Gastric	stomach
18	chr2:73965000-73973200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:73965000-73973200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:73965000-73978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:73965000-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:73965200-73966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:73965200-73966800	Weak transcription	Lung	lung
24	chr2:73965200-73968600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:73965200-73968600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:73965200-73968800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:73965200-73971200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:73965200-73973200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:73965200-73973400	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:73965200-73973800	Weak transcription	K562	blood
31	chr2:73965400-73966200	Weak transcription	Fetal Brain Female	brain
32	chr2:73965400-73966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:73965400-73966400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:73965400-73966600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:73965400-73966600	Weak transcription	Brain Angular Gyrus	brain
36	chr2:73965400-73966800	Weak transcription	Spleen	Spleen
37	chr2:73965400-73967800	Weak transcription	Brain Anterior Caudate	brain
38	chr2:73965400-73968400	Weak transcription	Primary T cells from cord blood	blood
39	chr2:73965400-73968400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:73965400-73968400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:73965400-73968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:73965400-73968600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:73965400-73968600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:73965400-73968600	Weak transcription	HSMM	muscle
45	chr2:73965400-73968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:73965400-73968800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:73965400-73968800	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:73965400-73968800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:73965400-73968800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:73965400-73968800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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