Variant report

Variant	rs721572
Chromosome Location	chr3:143698754-143698755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143694211..143696611-chr3:143698183..143700521,4	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1025984	0.80[CHD][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs10513234	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10513235	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11914731	0.86[EUR][1000 genomes]
rs13078840	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081286	0.86[EUR][1000 genomes]
rs1466941	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap]
rs16854772	0.92[ASN][1000 genomes]
rs17602500	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs17667256	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979910	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1992093	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2011080	0.85[EUR][1000 genomes]
rs2279856	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35085196	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35692092	0.84[ASN][1000 genomes]
rs35716467	0.83[ASN][1000 genomes]
rs35877644	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4527375	0.86[EUR][1000 genomes]
rs4561830	0.86[EUR][1000 genomes]
rs4613453	0.86[EUR][1000 genomes]
rs4616638	0.86[EUR][1000 genomes]
rs6440210	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.96[ASN][1000 genomes]
rs6440212	0.85[EUR][1000 genomes]
rs6768153	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6795008	0.86[EUR][1000 genomes]
rs6796460	0.85[EUR][1000 genomes]
rs723491	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7610378	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs7611326	0.86[EUR][1000 genomes]
rs7634145	0.85[EUR][1000 genomes]
rs7639366	0.85[EUR][1000 genomes]
rs7642551	0.86[EUR][1000 genomes]
rs7650145	0.81[EUR][1000 genomes]
rs7650172	0.86[EUR][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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs721572	TM4SF18	cis	cerebellum	SCAN
rs721572	CHST2	cis	parietal	SCAN
rs721572	HPS3	cis	cerebellum	SCAN
rs721572	C3orf58	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143692600-143707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
3	chr3:143693400-143699400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:143693400-143706800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:143693400-143708400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:143693400-143708400	Weak transcription	Psoas Muscle	Psoas
7	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:143693600-143711600	Weak transcription	Left Ventricle	heart
9	chr3:143693800-143701600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:143694000-143708000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:143694200-143703200	Weak transcription	Placenta	Placenta
12	chr3:143694200-143705600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:143694400-143700000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:143694400-143708400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:143694400-143718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:143694400-143719400	Weak transcription	Hela-S3	cervix
17	chr3:143694800-143707200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:143695000-143699000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:143695600-143699200	Enhancers	HSMM	muscle
20	chr3:143695600-143710200	Weak transcription	Fetal Brain Male	brain
21	chr3:143695600-143716800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:143696200-143699000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:143696200-143699000	Enhancers	Brain Substantia Nigra	brain
24	chr3:143696200-143703800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:143696400-143698800	Enhancers	Brain Cingulate Gyrus	brain
26	chr3:143696400-143698800	Enhancers	Osteobl	bone
27	chr3:143696400-143699000	Enhancers	Brain Angular Gyrus	brain
28	chr3:143696400-143711600	Weak transcription	Fetal Brain Female	brain
29	chr3:143696400-143711800	Weak transcription	Fetal Intestine Large	intestine
30	chr3:143696600-143698800	Active TSS	GM12878-XiMat	blood
31	chr3:143696600-143699400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:143696600-143704400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:143696800-143702800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:143696800-143706600	Weak transcription	Ovary	ovary
35	chr3:143697000-143699000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:143697000-143699000	Enhancers	NHLF	lung
37	chr3:143697000-143699200	Weak transcription	Right Atrium	heart
38	chr3:143697000-143701400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:143697000-143701600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:143697000-143708000	Weak transcription	HUVEC	blood vessel
41	chr3:143697000-143708400	Weak transcription	K562	blood
42	chr3:143697000-143713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:143697000-143722800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:143697000-143729200	Weak transcription	Aorta	Aorta
45	chr3:143697200-143698800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:143697200-143698800	Weak transcription	Fetal Heart	heart
47	chr3:143697200-143699400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:143697200-143708400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:143697200-143708400	Weak transcription	HMEC	breast
50	chr3:143697200-143708400	Weak transcription	NHEK	skin

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