Variant report

Variant	rs9869437
Chromosome Location	chr3:196228360-196228361
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196228328..196231500-chr3:196241253..196244010,3	MCF-7	breast:
2	chr3:196158149..196160918-chr3:196228046..196230093,2	K562	blood:
3	chr3:196158147..196160918-chr3:196228046..196230490,2	K562	blood:
4	chr3:196228243..196229993-chr3:196279816..196281934,2	MCF-7	breast:
5	chr3:196228123..196230544-chr3:196269103..196271110,2	MCF-7	breast:
6	chr3:196054872..196057138-chr3:196227517..196230475,2	K562	blood:
7	chr3:196062616..196065996-chr3:196228027..196230994,3	K562	blood:
8	chr3:196138176..196140569-chr3:196226942..196228528,2	MCF-7	breast:
9	chr3:196156342..196159977-chr3:196227568..196231019,3	MCF-7	breast:
10	chr3:196225951..196229671-chr3:196232919..196236791,4	K562	blood:
11	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:
12	chr3:196215382..196218284-chr3:196226840..196230501,3	K562	blood:
13	chr3:196014060..196015783-chr3:196226858..196228542,2	K562	blood:
14	chr3:196228360..196230517-chr3:196253660..196255991,2	MCF-7	breast:
15	chr3:196228000..196230318-chr3:196411872..196414109,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000213358	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000214097	Chromatin interaction
ENSG00000174013	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000185798	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11185543	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11718980	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719920	0.82[EUR][1000 genomes]
rs12635457	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13084212	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13098146	0.94[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13099664	0.93[ASN][1000 genomes]
rs34196595	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34547573	0.86[ASN][1000 genomes]
rs34722299	0.88[EUR][1000 genomes]
rs3796129	0.81[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4244200	0.87[ASN][1000 genomes]
rs4393941	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4916431	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4916499	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6775484	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71630192	0.92[EUR][1000 genomes]
rs7430950	0.87[CHD][hapmap];0.86[ASN][1000 genomes]
rs7611980	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7612450	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7643192	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7646174	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7646273	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7647487	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9837291	0.81[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9837568	0.88[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9843876	0.87[ASN][1000 genomes]
rs9844068	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9856006	0.87[ASN][1000 genomes]
rs9864836	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9869437	TCTEX1D2	cis	parietal	SCAN
rs9869437	RNF168	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196225800-196231600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:196226400-196231000	Active TSS	GM12878-XiMat	blood
3	chr3:196226400-196231200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:196226800-196228800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:196226800-196231200	Active TSS	Colonic Mucosa	Colon
6	chr3:196227000-196228400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:196227000-196229800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:196227000-196230800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:196227000-196231000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr3:196227000-196231000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:196227000-196231000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:196227000-196231000	Active TSS	Esophagus	oesophagus
13	chr3:196227000-196231200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr3:196227000-196231200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:196227000-196231200	Active TSS	Fetal Kidney	kidney
16	chr3:196227000-196231200	Active TSS	Rectal Smooth Muscle	rectum
17	chr3:196227200-196229200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr3:196227200-196230600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:196227200-196230800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:196227200-196230800	Active TSS	Gastric	stomach
21	chr3:196227200-196231000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:196227200-196231000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:196227200-196231000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:196227200-196231000	Active TSS	Lung	lung
25	chr3:196227200-196231000	Active TSS	HMEC	breast
26	chr3:196227200-196231200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:196227200-196231200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:196227200-196231200	Active TSS	Brain Angular Gyrus	brain
29	chr3:196227200-196231400	Active TSS	Fetal Muscle Trunk	muscle
30	chr3:196227200-196231600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:196227400-196228400	Active TSS	Fetal Thymus	thymus
32	chr3:196227400-196228600	Bivalent/Poised TSS	HepG2	liver
33	chr3:196227400-196228800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:196227400-196229000	Weak transcription	Spleen	Spleen
35	chr3:196227400-196229200	Active TSS	Brain Germinal Matrix	brain
36	chr3:196227400-196229800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr3:196227400-196230200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:196227400-196230600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:196227400-196230600	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr3:196227400-196230600	Active TSS	Stomach Mucosa	stomach
41	chr3:196227400-196230800	Active TSS	Fetal Intestine Large	intestine
42	chr3:196227400-196230800	Active TSS	Dnd41	blood
43	chr3:196227400-196230800	Active TSS	NHEK	skin
44	chr3:196227400-196231000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:196227400-196231000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr3:196227400-196231000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:196227400-196231000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:196227400-196231000	Active TSS	Aorta	Aorta
49	chr3:196227400-196231000	Active TSS	Colon Smooth Muscle	Colon
50	chr3:196227400-196231000	Active TSS	Duodenum Smooth Muscle	Duodenum

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