Variant report

Variant	rs2306124
Chromosome Location	chr1:155059851-155059852
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154970467..154977420-chr1:155052491..155060843,19	MCF-7	breast:
2	chr1:155055553..155060043-chr1:155139937..155145817,8	K562	blood:
3	chr1:155056284..155060443-chr1:155143066..155147437,8	MCF-7	breast:
4	chr1:155057862..155060802-chr1:155145958..155147519,2	K562	blood:
5	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
6	chr1:154529703..154532693-chr1:155057067..155059987,2	K562	blood:
7	chr1:154972694..154975957-chr1:155059383..155061597,3	MCF-7	breast:
8	chr1:155058008..155061537-chr1:155106258..155110440,4	K562	blood:
9	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
10	chr1:155059848..155062342-chr1:155144360..155146829,2	MCF-7	breast:
11	chr1:154931665..154935409-chr1:155055892..155060477,8	MCF-7	breast:
12	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:
13	chr1:155020796..155024695-chr1:155055166..155059924,7	K562	blood:
14	chr1:155059639..155063596-chr1:155149285..155151101,3	MCF-7	breast:
15	chr1:154941529..154944421-chr1:155058402..155060354,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160685	Chromatin interaction
ENSG00000163348	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000202027	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000169242	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes]
rs10157801	0.85[JPT][hapmap]
rs10796938	1.00[ASN][1000 genomes]
rs10796939	0.90[ASN][1000 genomes]
rs10908454	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908455	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908456	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11264307	0.81[AFR][1000 genomes]
rs11264311	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11264312	1.00[ASN][1000 genomes]
rs11264313	0.97[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264321	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264322	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11264327	0.93[ASN][1000 genomes]
rs11264328	0.93[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.97[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12047986	0.86[AFR][1000 genomes]
rs12145362	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1870939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	1.00[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4361977	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4625273	1.00[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	1.00[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	1.00[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7366138	0.95[ASN][1000 genomes]
rs7366355	1.00[ASN][1000 genomes]
rs7367207	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7367758	0.97[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7534162	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9297	0.85[JPT][hapmap]
rs9330263	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2306124	SMCP	cis	cerebellum	SCAN
rs2306124	RPRD2	cis	parietal	SCAN
rs2306124	UBE2Q1	cis	cerebellum	SCAN
rs2306124	SCARNA4	cis	cerebellum	SCAN
rs2306124	APOA1BP	cis	cerebellum	SCAN
rs2306124	SETDB1	cis	parietal	SCAN
rs2306124	DENND4B	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155058200-155060200	Enhancers	Fetal Heart	heart
2	chr1:155058400-155060000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:155058400-155063800	Weak transcription	HSMM	muscle
4	chr1:155058600-155063800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155058600-155063800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:155058600-155063800	Weak transcription	HUVEC	blood vessel
7	chr1:155058600-155066000	Weak transcription	Right Atrium	heart
8	chr1:155059000-155060000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:155059000-155060400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:155059000-155063400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:155059000-155063600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:155059000-155063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:155059000-155063600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:155059000-155063600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:155059000-155063600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:155059000-155063600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:155059000-155063600	Weak transcription	Liver	Liver
18	chr1:155059000-155063600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:155059000-155063600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:155059000-155063600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:155059000-155063600	Weak transcription	Brain Substantia Nigra	brain
22	chr1:155059000-155063600	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:155059000-155063600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:155059000-155063600	Weak transcription	Pancreas	Pancrea
25	chr1:155059000-155063600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:155059000-155063600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:155059000-155063600	Weak transcription	Stomach Mucosa	stomach
28	chr1:155059000-155063600	Weak transcription	NHEK	skin
29	chr1:155059000-155063800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:155059000-155063800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:155059000-155063800	Weak transcription	Brain Angular Gyrus	brain
32	chr1:155059000-155063800	Weak transcription	Fetal Brain Female	brain
33	chr1:155059000-155063800	Weak transcription	Gastric	stomach
34	chr1:155059000-155063800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:155059000-155063800	Weak transcription	GM12878-XiMat	blood
36	chr1:155059000-155064200	Weak transcription	Left Ventricle	heart
37	chr1:155059000-155066200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:155059200-155060200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:155059200-155063600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:155059200-155063600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:155059200-155063600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:155059200-155063600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:155059200-155063600	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:155059200-155063600	Weak transcription	Colonic Mucosa	Colon
45	chr1:155059200-155063600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:155059200-155063600	Weak transcription	Right Ventricle	heart
47	chr1:155059200-155063600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:155059200-155063600	Weak transcription	HMEC	breast
49	chr1:155059200-155063800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:155059200-155063800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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