Variant report

Variant	rs4653589
Chromosome Location	chr1:224688598-224688599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224683423..224687942-chr1:224688283..224691740,8	K562	blood:
2	chr1:224688139..224690298-chr1:225044581..225047366,2	K562	blood:
3	chr1:224622043..224623637-chr1:224687364..224688891,2	MCF-7	breast:
4	chr1:224688210..224692730-chr1:224708810..224713777,4	K562	blood:
5	chr1:224622250..224624534-chr1:224688167..224691066,2	MCF-7	breast:
6	chr1:224645897..224648212-chr1:224688548..224690344,2	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10753474	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916626	0.93[ASN][1000 genomes]
rs10916628	0.90[EUR][1000 genomes]
rs10916629	0.83[EUR][1000 genomes]
rs10916631	0.87[EUR][1000 genomes]
rs10916632	0.87[EUR][1000 genomes]
rs12093242	0.87[EUR][1000 genomes]
rs12140117	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140906	0.85[EUR][1000 genomes]
rs12141016	0.85[ASN][1000 genomes]
rs12141708	0.87[EUR][1000 genomes]
rs12142949	0.88[EUR][1000 genomes]
rs12566578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1891243	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1891244	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2648743	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738367	0.87[EUR][1000 genomes]
rs4294381	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap]
rs59319739	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61825792	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426133	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6665956	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6688146	0.89[EUR][1000 genomes]
rs6695773	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6699035	0.87[EUR][1000 genomes]
rs712065	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs712066	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541723	0.87[EUR][1000 genomes]
rs7541917	0.88[EUR][1000 genomes]
rs7545252	0.90[EUR][1000 genomes]
rs7550648	0.87[EUR][1000 genomes]
rs791504	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653589	CNIH3	cis	cerebellum	SCAN
rs4653589	BPNT1	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224679800-224689600	Weak transcription	Pancreas	Pancrea
2	chr1:224682800-224690200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:224685200-224688600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:224685200-224695800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:224685600-224689600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:224686000-224689600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:224686000-224690000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:224686200-224689000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:224686400-224689600	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:224686600-224688800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:224686600-224688800	Enhancers	NHLF	lung
12	chr1:224686600-224689600	Weak transcription	Esophagus	oesophagus
13	chr1:224686600-224689800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:224686600-224689800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:224686600-224689800	Weak transcription	Fetal Lung	lung
16	chr1:224686600-224689800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:224686600-224690000	Weak transcription	Aorta	Aorta
18	chr1:224686600-224690000	Weak transcription	Liver	Liver
19	chr1:224686600-224690200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:224686600-224690200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:224686600-224691000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:224686600-224691000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:224686600-224691200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:224686600-224691200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:224686800-224689000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:224686800-224689000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:224686800-224689400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:224686800-224689600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:224686800-224689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:224686800-224689600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:224686800-224689600	Weak transcription	Colonic Mucosa	Colon
32	chr1:224686800-224689600	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:224686800-224689600	Weak transcription	Gastric	stomach
34	chr1:224686800-224689600	Weak transcription	Left Ventricle	heart
35	chr1:224686800-224689600	Weak transcription	Lung	lung
36	chr1:224686800-224689600	Weak transcription	Right Atrium	heart
37	chr1:224686800-224689600	Weak transcription	Right Ventricle	heart
38	chr1:224686800-224689600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:224686800-224689600	Weak transcription	Stomach Mucosa	stomach
40	chr1:224686800-224689800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:224686800-224690000	Weak transcription	Ovary	ovary
42	chr1:224686800-224690000	Weak transcription	Psoas Muscle	Psoas
43	chr1:224686800-224690000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:224686800-224690000	Weak transcription	Spleen	Spleen
45	chr1:224686800-224690200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:224686800-224690200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:224686800-224690600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:224686800-224691000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:224686800-224691000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:224686800-224691000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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