Variant report

Variant	rs16855022
Chromosome Location	chr1:179927135-179927136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:179927033-179927241	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:
2	chr1:179892500..179895461-chr1:179925642..179927756,2	K562	blood:
3	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
4	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
5	chr1:179921415..179925789-chr1:179925828..179929752,13	MCF-7	breast:
6	chr1:179890847..179892932-chr1:179926143..179929567,3	K562	blood:
7	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260360	TF binding region
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000235145	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10442618	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10494524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913920	0.83[EUR][1000 genomes]
rs12118985	0.92[ASN][1000 genomes]
rs12120418	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12121834	0.92[ASN][1000 genomes]
rs12121845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[ASN][1000 genomes]
rs12123139	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123201	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125556	0.92[ASN][1000 genomes]
rs12125693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12125893	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12126967	0.84[TSI][hapmap]
rs12130397	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130673	0.83[EUR][1000 genomes]
rs12130675	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131200	0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12132694	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133136	0.83[EUR][1000 genomes]
rs12134536	0.92[ASN][1000 genomes]
rs12135751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135828	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138201	0.92[ASN][1000 genomes]
rs12138974	0.92[ASN][1000 genomes]
rs12139323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139761	0.92[ASN][1000 genomes]
rs12140235	0.92[ASN][1000 genomes]
rs12140589	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12141134	0.80[TSI][hapmap]
rs12141817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144275	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144346	0.84[TSI][hapmap]
rs12144352	0.84[TSI][hapmap]
rs12145411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16843139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16854997	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855014	0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16855019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855021	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855025	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855049	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855052	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855070	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855099	0.84[ASN][1000 genomes]
rs16855103	0.84[ASN][1000 genomes]
rs16855107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855110	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855130	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855144	0.84[ASN][1000 genomes]
rs16855259	0.84[ASN][1000 genomes]
rs16855268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16855270	0.92[ASN][1000 genomes]
rs16855286	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16855289	0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17299006	0.83[EUR][1000 genomes]
rs17371159	0.84[TSI][hapmap]
rs17371308	0.84[TSI][hapmap]
rs3856048	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267622	0.84[ASN][1000 genomes]
rs4266842	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4278337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4460595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652469	0.81[CHD][hapmap]
rs57165548	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58316647	0.92[ASN][1000 genomes]
rs58463801	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58749862	0.92[ASN][1000 genomes]
rs58844263	0.84[ASN][1000 genomes]
rs59132689	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60064848	0.84[ASN][1000 genomes]
rs60895715	0.84[ASN][1000 genomes]
rs60927554	0.84[ASN][1000 genomes]
rs60972670	0.92[ASN][1000 genomes]
rs60976015	0.84[ASN][1000 genomes]
rs61014689	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61242295	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73032352	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032390	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73032397	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73034408	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73034486	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73039990	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039999	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040001	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525395	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7556630	0.85[ASN][1000 genomes]
rs9699897	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701232	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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 miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16855022	CPNE7	trans	cerebellum	SCAN
rs16855022	RALGPS2	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179923600-179928000	Active TSS	GM12878-XiMat	blood
2	chr1:179924800-179935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:179924800-179937800	Weak transcription	Spleen	Spleen
4	chr1:179924800-179938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:179924800-179938000	Weak transcription	Lung	lung
6	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:179925200-179927600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:179925200-179928200	Weak transcription	Left Ventricle	heart
9	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
10	chr1:179925400-179927200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:179925400-179927600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:179925400-179927800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:179925400-179927800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:179925400-179928400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:179925400-179929800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:179925400-179931000	Weak transcription	Fetal Thymus	thymus
17	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:179925600-179927200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:179925600-179928000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:179925600-179928000	Enhancers	Fetal Heart	heart
21	chr1:179925600-179930200	Weak transcription	Fetal Stomach	stomach
22	chr1:179925600-179935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:179925600-179938400	Weak transcription	HSMM	muscle
24	chr1:179925800-179927200	Enhancers	Brain Anterior Caudate	brain
25	chr1:179925800-179927200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:179925800-179927200	Enhancers	Hela-S3	cervix
27	chr1:179925800-179927200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:179925800-179927800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:179925800-179927800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:179925800-179927800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:179925800-179927800	Enhancers	Adipose Nuclei	Adipose
32	chr1:179925800-179927800	Enhancers	HUVEC	blood vessel
33	chr1:179925800-179928200	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:179925800-179929600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:179925800-179929800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:179925800-179930200	Weak transcription	Fetal Intestine Small	intestine
37	chr1:179925800-179930600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:179925800-179933400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:179925800-179935600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:179925800-179935600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:179925800-179937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:179925800-179937600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:179925800-179937600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:179925800-179937800	Weak transcription	Thymus	Thymus
45	chr1:179925800-179940600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:179926000-179927400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:179926000-179927800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr1:179926000-179928400	Weak transcription	Psoas Muscle	Psoas
49	chr1:179926000-179931600	Weak transcription	Ovary	ovary
50	chr1:179926000-179937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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