Variant report

Variant	rs12971201
Chromosome Location	chr18:12830538-12830539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12828774..12831402-chr18:12837889..12840391,3	K562	blood:
2	chr18:12828322..12831138-chr18:12840909..12843009,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12957037	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2542152	0.88[YRI][hapmap]
rs2542157	0.86[GIH][hapmap];0.88[YRI][hapmap]
rs2542160	0.96[GIH][hapmap]
rs2542162	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847273	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847281	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847286	0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs2847298	0.87[YRI][hapmap]
rs2852151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826557	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478582	1.00[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4797709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs559406	1.00[ASN][1000 genomes]
rs588447	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs592390	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs641085	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs674222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087237	1.00[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs888271	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
7	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12971201	PTPN2	cis	parietal	SCAN
rs12971201	FAM71E2	trans	parietal	SCAN
rs12971201	FAM38B	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
2	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
3	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
5	chr18:12809600-12833200	Weak transcription	HSMM	muscle
6	chr18:12809600-12838200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr18:12809600-12838200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr18:12812000-12838400	Weak transcription	Right Ventricle	heart
9	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr18:12817400-12833400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:12817800-12837600	Weak transcription	NH-A	brain
12	chr18:12820000-12836400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr18:12820400-12838600	Weak transcription	Brain Angular Gyrus	brain
14	chr18:12820800-12830800	Weak transcription	Lung	lung
15	chr18:12820800-12837600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:12820800-12838200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:12820800-12838200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:12821000-12833400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr18:12821000-12840400	Weak transcription	Brain Substantia Nigra	brain
20	chr18:12821400-12834000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr18:12821400-12836800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr18:12821600-12839200	Weak transcription	Brain Anterior Caudate	brain
23	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:12822000-12832200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr18:12822600-12832000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr18:12822800-12833400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr18:12823000-12837600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr18:12823400-12836200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12824200-12831400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr18:12824200-12835000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr18:12825400-12833000	Weak transcription	HSMMtube	muscle
32	chr18:12825400-12838200	Weak transcription	Gastric	stomach
33	chr18:12825400-12840400	Weak transcription	Spleen	Spleen
34	chr18:12825600-12838200	Weak transcription	Aorta	Aorta
35	chr18:12825600-12838200	Weak transcription	K562	blood
36	chr18:12826000-12838400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr18:12826400-12837800	Weak transcription	Fetal Brain Male	brain
38	chr18:12826600-12831000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr18:12826800-12838200	Weak transcription	Pancreas	Pancrea
40	chr18:12827000-12831600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:12827200-12836600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:12827600-12833400	Weak transcription	Left Ventricle	heart
43	chr18:12827600-12838200	Weak transcription	Esophagus	oesophagus
44	chr18:12827600-12838200	Weak transcription	Small Intestine	intestine
45	chr18:12827600-12838400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr18:12827600-12843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr18:12827800-12836200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr18:12828000-12831800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr18:12828200-12831200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr18:12828200-12833200	Weak transcription	Colon Smooth Muscle	Colon

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