Variant report

Variant	rs1441092
Chromosome Location	chr2:234267619-234267620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234262927..234266874-chr2:234267273..234270022,5	MCF-7	breast:
2	chr2:234265828..234267966-chr2:234273023..234275764,2	K562	blood:
3	chr2:234266865..234268565-chr2:234269887..234272310,2	K562	blood:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10165561	0.82[JPT][hapmap]
rs10187822	0.83[JPT][hapmap]
rs10192702	0.83[JPT][hapmap]
rs10195395	0.83[JPT][hapmap]
rs10210302	0.83[JPT][hapmap]
rs1045100	0.83[JPT][hapmap]
rs10929110	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10929322	0.83[JPT][hapmap]
rs11679791	0.83[JPT][hapmap]
rs12162308	0.82[JPT][hapmap]
rs12373747	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12994971	0.83[JPT][hapmap]
rs12994997	0.83[JPT][hapmap]
rs13009506	0.83[JPT][hapmap]
rs13015823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13035837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391356	0.83[JPT][hapmap]
rs13411660	0.83[JPT][hapmap]
rs2241878	0.83[JPT][hapmap]
rs2241879	0.83[JPT][hapmap]
rs2241880	0.83[JPT][hapmap]
rs2289472	0.83[JPT][hapmap]
rs2289474	0.83[JPT][hapmap]
rs2289477	0.83[JPT][hapmap]
rs34231016	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34515783	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34689708	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762588	0.81[JPT][hapmap]
rs3792108	0.83[JPT][hapmap]
rs3792109	0.83[JPT][hapmap]
rs3792111	0.83[JPT][hapmap]
rs3792112	0.83[JPT][hapmap]
rs3828309	0.83[JPT][hapmap]
rs55664157	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56201966	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56263467	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60485593	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6431654	0.83[JPT][hapmap]
rs6431660	0.81[JPT][hapmap]
rs6708373	0.83[JPT][hapmap]
rs6752107	0.83[JPT][hapmap]
rs67863435	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559194	0.83[JPT][hapmap]

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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv1820563	chr2:234263212-234282210	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1441092	EFHD1	cis	parietal	SCAN
rs1441092	NPPC	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234263800-234268400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr2:234263800-234268400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr2:234264000-234267800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr2:234264400-234268800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:234264400-234268800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:234264400-234269000	Weak transcription	NHLF	lung
7	chr2:234264400-234269600	Weak transcription	Aorta	Aorta
8	chr2:234264400-234274800	Weak transcription	NHDF-Ad	bronchial
9	chr2:234264400-234287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:234264600-234272400	Weak transcription	HUVEC	blood vessel
11	chr2:234264600-234290800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:234264800-234268000	Enhancers	Adipose Nuclei	Adipose
14	chr2:234264800-234268400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:234264800-234268600	Weak transcription	K562	blood
16	chr2:234264800-234269000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:234264800-234269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:234264800-234271400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:234264800-234272200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:234264800-234289200	Weak transcription	Esophagus	oesophagus
21	chr2:234264800-234292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:234265000-234268000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:234265000-234268200	Enhancers	Colon Smooth Muscle	Colon
24	chr2:234265000-234268600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:234265000-234272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:234265000-234283800	Weak transcription	Thymus	Thymus
27	chr2:234265000-234295000	Weak transcription	Osteobl	bone
28	chr2:234265200-234269600	Weak transcription	Fetal Intestine Small	intestine
29	chr2:234265200-234269800	Weak transcription	Brain Angular Gyrus	brain
30	chr2:234265200-234269800	Weak transcription	Psoas Muscle	Psoas
31	chr2:234265200-234284000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:234265200-234295000	Weak transcription	NH-A	brain
33	chr2:234265400-234281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:234265600-234269200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:234265800-234269200	Weak transcription	Fetal Heart	heart
36	chr2:234265800-234270200	Weak transcription	NHEK	skin
37	chr2:234265800-234272200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:234265800-234272200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:234265800-234272200	Weak transcription	Fetal Lung	lung
40	chr2:234265800-234272400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:234265800-234272400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:234265800-234278200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:234265800-234278200	Weak transcription	Brain Germinal Matrix	brain
44	chr2:234265800-234283800	Weak transcription	Colonic Mucosa	Colon
45	chr2:234265800-234289400	Weak transcription	Hela-S3	cervix
46	chr2:234265800-234293000	Weak transcription	HMEC	breast
47	chr2:234266000-234267800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:234266000-234268000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:234266000-234268200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr2:234266000-234268600	Weak transcription	H1 Cell Line	embryonic stem cell

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