Variant report

Variant	rs4652366
Chromosome Location	chr1:179323919-179323920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179050571..179052997-chr1:179322581..179325112,2	MCF-7	breast:
2	chr1:179321788..179324308-chr1:179333616..179335747,3	MCF-7	breast:
3	chr1:179323629..179325492-chr1:179329945..179332466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186283	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10913728	0.83[JPT][hapmap]
rs10913736	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11577489	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11581507	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11799784	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11804234	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11804236	0.95[ASN][1000 genomes]
rs13306727	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13306730	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16853998	0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16854003	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17369088	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2152320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2184575	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45471092	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651024	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs55906130	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55986478	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56149964	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56303406	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57864135	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6425534	0.96[ASN][1000 genomes]
rs6666358	0.89[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs6666455	0.84[GIH][hapmap]
rs6673354	0.83[ASN][1000 genomes]
rs6682068	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67545145	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68098532	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534976	0.81[EUR][1000 genomes];1.00[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv1804302	chr1:179315357-179333194	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv548277	chr1:179319868-179333194	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1809332	chr1:179320578-179333194	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv548278	chr1:179323919-179333194	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4652366	AXDND1	cis	Thyroid	GTEx
rs4652366	RASAL2	cis	parietal	SCAN
rs4652366	TDRD5	cis	Artery Aorta	GTEx
rs4652366	TDRD5	cis	parietal	SCAN
rs4652366	AXDND1	cis	Nerve Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:179294200-179324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
5	chr1:179298600-179324200	Weak transcription	Thymus	Thymus
6	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:179303200-179324600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:179304200-179324400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:179304200-179324400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:179304200-179324600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:179304200-179325200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:179304400-179324400	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:179304600-179324200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:179305200-179327200	Weak transcription	Right Ventricle	heart
15	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea
16	chr1:179306800-179324600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:179307400-179325800	Weak transcription	Esophagus	oesophagus
18	chr1:179307600-179325200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:179308000-179324400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:179309800-179326400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:179310000-179325200	Strong transcription	Primary T cells from cord blood	blood
22	chr1:179310400-179324400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:179311200-179325200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:179311600-179326400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:179312000-179324200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:179312000-179324800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:179312200-179325200	Strong transcription	Liver	Liver
28	chr1:179312600-179334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:179314600-179326200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:179314800-179327800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:179314800-179334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:179315000-179324600	Weak transcription	Spleen	Spleen
33	chr1:179315000-179334400	Weak transcription	Brain Substantia Nigra	brain
34	chr1:179315000-179334400	Weak transcription	Left Ventricle	heart
35	chr1:179315400-179334400	Weak transcription	Fetal Kidney	kidney
36	chr1:179315600-179334400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:179315800-179334200	Weak transcription	Fetal Thymus	thymus
38	chr1:179316000-179327600	Weak transcription	Brain Angular Gyrus	brain
39	chr1:179316000-179334000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:179316000-179334200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:179316000-179334400	Weak transcription	Fetal Brain Female	brain
42	chr1:179316000-179334400	Weak transcription	Ovary	ovary
43	chr1:179316200-179324600	Weak transcription	Psoas Muscle	Psoas
44	chr1:179316400-179332800	Weak transcription	Fetal Intestine Small	intestine
45	chr1:179316800-179324400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:179317000-179324200	Strong transcription	Hela-S3	cervix
47	chr1:179317600-179334400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:179317800-179327800	Weak transcription	NHEK	skin
49	chr1:179319200-179324200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:179319200-179334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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