Variant report

Variant	rs743185
Chromosome Location	chr22:29103217-29103218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29103207..29105613-chr22:29137554..29139656,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1884816	0.92[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884817	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2014114	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2017309	0.90[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs2347443	0.88[CEU][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28483387	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752777	0.92[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752785	0.84[GIH][hapmap];0.82[YRI][hapmap]
rs5762766	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs6519761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714191	0.84[GIH][hapmap];0.87[MEX][hapmap]
rs7289973	0.84[EUR][1000 genomes];0.80[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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	83 gene(s)	inside rSNPs	diseases
2	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active 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	7 gene(s)	inside rSNPs	diseases
3	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1064624	chr22:29065528-29130728	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv513775	chr22:29083731-29137822	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs743185	ASPHD2	cis	parietal	SCAN
rs743185	SNRPD3	cis	parietal	SCAN
rs743185	RGL4	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
2	chr22:29076400-29105000	Weak transcription	HUVEC	blood vessel
3	chr22:29076400-29105200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:29076400-29105800	Weak transcription	NHLF	lung
5	chr22:29076400-29119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:29076400-29129400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr22:29077200-29105000	Weak transcription	Osteobl	bone
8	chr22:29077400-29106000	Weak transcription	A549	lung
9	chr22:29079600-29130200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr22:29082200-29109800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr22:29082800-29106000	Weak transcription	Liver	Liver
12	chr22:29082800-29137600	Weak transcription	Spleen	Spleen
13	chr22:29083000-29126600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:29083600-29104000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:29085000-29116600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr22:29085800-29105000	Weak transcription	HMEC	breast
17	chr22:29086200-29106600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr22:29086400-29106000	Weak transcription	HSMM	muscle
19	chr22:29087800-29106200	Weak transcription	Fetal Lung	lung
20	chr22:29088600-29118600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr22:29090200-29129000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr22:29090400-29106000	Weak transcription	HSMMtube	muscle
23	chr22:29090400-29110800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:29090600-29137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:29090600-29137200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr22:29090800-29108000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr22:29091000-29104000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr22:29091000-29116600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr22:29091000-29120200	Weak transcription	Placenta	Placenta
30	chr22:29092000-29108600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:29092600-29106200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr22:29093600-29121800	Weak transcription	Small Intestine	intestine
33	chr22:29093600-29132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr22:29093800-29126600	Weak transcription	Gastric	stomach
35	chr22:29094600-29125000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr22:29095200-29114600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr22:29096000-29106200	Weak transcription	Fetal Muscle Leg	muscle
38	chr22:29096600-29106200	Weak transcription	K562	blood
39	chr22:29097000-29130800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr22:29097200-29105000	Strong transcription	Fetal Stomach	stomach
41	chr22:29098400-29105800	Weak transcription	NHDF-Ad	bronchial
42	chr22:29098600-29108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr22:29098800-29111400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr22:29099000-29109600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr22:29099400-29109800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr22:29099800-29105600	Weak transcription	Fetal Thymus	thymus
47	chr22:29099800-29106000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr22:29099800-29129000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr22:29100200-29104000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr22:29100400-29137200	Weak transcription	Pancreas	Pancrea

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