Variant report

Variant	rs792433
Chromosome Location	chr1:212502157-212502158
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	chr1:212486882..212489433-chr1:212500849..212503303,2	K562	blood:
2	chr1:212497077..212499015-chr1:212500342..212502392,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM206-3	chr1:212497766-212502930	l_184_chr1:212497765-212519010_heart

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10779576	0.82[CHB][hapmap]
rs1086892	1.00[ASW][hapmap]
rs12725070	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1444692	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472225	0.82[CHB][hapmap]
rs1774252	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2921127	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2921128	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2921129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2995255	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2995256	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2995257	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2995258	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099111	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3121291	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351383	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351392	0.86[GIH][hapmap]
rs351395	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351397	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351413	0.81[GIH][hapmap]
rs351416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs351420	0.80[EUR][1000 genomes]
rs4554777	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951584	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs6674587	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs701906	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs701907	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs701908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792434	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792440	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792441	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792442	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs812074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1806604	chr1:212468974-212505860	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs792433	IRF6	cis	parietal	SCAN
rs792433	IL24	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
2	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:212467400-212526000	Weak transcription	A549	lung
5	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
7	chr1:212484000-212503000	Weak transcription	Fetal Stomach	stomach
8	chr1:212484000-212506600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:212484200-212507000	Weak transcription	HepG2	liver
10	chr1:212484400-212502800	Weak transcription	Thymus	Thymus
11	chr1:212484400-212506800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:212484600-212507200	Weak transcription	Right Ventricle	heart
13	chr1:212484800-212503000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:212486000-212504000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:212486000-212507000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:212486200-212526000	Weak transcription	HUVEC	blood vessel
17	chr1:212486600-212502200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:212486600-212506800	Weak transcription	Ovary	ovary
19	chr1:212486800-212503600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:212487200-212506600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:212488000-212502600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:212489000-212502400	Weak transcription	GM12878-XiMat	blood
23	chr1:212489600-212506800	Weak transcription	NHDF-Ad	bronchial
24	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
25	chr1:212489800-212503400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:212489800-212505400	Weak transcription	Fetal Lung	lung
27	chr1:212489800-212506800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:212489800-212506800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:212490000-212507800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:212491600-212502800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:212491800-212502600	Weak transcription	Hela-S3	cervix
32	chr1:212492400-212506800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:212492800-212502600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:212492800-212504400	Weak transcription	Adipose Nuclei	Adipose
35	chr1:212493000-212502800	Weak transcription	Primary B cells from cord blood	blood
36	chr1:212493600-212502800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:212493800-212506000	Weak transcription	K562	blood
38	chr1:212493800-212506800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:212493800-212507200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:212496000-212502800	Weak transcription	Fetal Intestine Large	intestine
42	chr1:212496400-212502800	Weak transcription	Fetal Thymus	thymus
43	chr1:212496800-212502600	Weak transcription	Dnd41	blood
44	chr1:212496800-212506400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:212497000-212507200	Weak transcription	Fetal Brain Female	brain
46	chr1:212497400-212502800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:212497600-212506800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:212497800-212502600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:212497800-212505400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:212497800-212505600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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