Variant report

Variant	rs34411239
Chromosome Location	chr3:93723952-93723953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:93722234..93724634-chr3:93733108..93735943,2	K562	blood:
2	chr3:93721000..93725762-chr3:93785860..93789650,5	MCF-7	breast:
3	chr3:93719824..93725075-chr3:93780190..93785120,6	MCF-7	breast:
4	chr3:93720544..93724631-chr3:93780488..93783673,7	MCF-7	breast:
5	chr3:93722699..93725451-chr3:93787826..93790801,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178694	Chromatin interaction
ENSG00000178700	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12492553	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13076476	0.84[ASW][hapmap]
rs13085785	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2965	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs34309901	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34557251	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35793773	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35815512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4426680	0.83[AFR][1000 genomes]
rs4857146	0.97[EUR][1000 genomes]
rs4857186	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs56982991	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6123	0.85[GIH][hapmap]
rs6764203	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6765621	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6777479	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6791811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7428007	0.80[EUR][1000 genomes]
rs7633544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7644769	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7653521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8178603	0.83[EUR][1000 genomes]
rs8178610	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8178613	0.80[EUR][1000 genomes]
rs8178616	0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap]
rs921727	0.81[CEU][hapmap]
rs9844676	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9872376	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002292	chr3:93519466-93736214	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
2	nsv998051	chr3:93519466-93740680	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	14 gene(s)	inside rSNPs	n/a
3	nsv1005328	chr3:93519466-93743921	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
4	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
5	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv533358	chr3:93575289-93745823	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
11	nsv916541	chr3:93575289-93758589	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
12	esv1803747	chr3:93602038-93759079	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
13	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
14	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
15	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	19 gene(s)	inside rSNPs	n/a
16	nsv1003434	chr3:93654100-93740824	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
17	nsv536647	chr3:93654100-93740824	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
18	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
19	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking 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	20 gene(s)	inside rSNPs	diseases
20	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
21	esv1792568	chr3:93706380-93759079	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
22	nsv590987	chr3:93708820-93779664	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34411239	STX19	cis	parietal	SCAN
rs34411239	WBP2NL	trans	cerebellum	SCAN
rs34411239	ARL6	cis	cerebellum	SCAN
rs34411239	DHFRL1	cis	cerebellum	SCAN
rs34411239	OR5K2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93699600-93762600	Weak transcription	Pancreas	Pancrea
2	chr3:93699800-93743400	Weak transcription	Aorta	Aorta
3	chr3:93699800-93746000	Weak transcription	Fetal Stomach	stomach
4	chr3:93700000-93732600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:93701000-93730600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:93701200-93724200	Weak transcription	Brain Anterior Caudate	brain
7	chr3:93701400-93725600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:93708400-93780800	Weak transcription	K562	blood
9	chr3:93708600-93762600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:93709200-93727600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:93713000-93726000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:93713200-93725600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:93713200-93742400	Weak transcription	Small Intestine	intestine
14	chr3:93713200-93743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:93713200-93762200	Weak transcription	HSMM	muscle
16	chr3:93713800-93736200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:93714200-93733400	Weak transcription	Primary T cells from cord blood	blood
18	chr3:93716200-93725200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:93716400-93725000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:93716600-93725400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:93717000-93763000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:93717800-93727200	Weak transcription	HepG2	liver
23	chr3:93718000-93742800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:93719600-93758000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:93721000-93725400	Weak transcription	Fetal Heart	heart
26	chr3:93721200-93763200	Weak transcription	Left Ventricle	heart
27	chr3:93721400-93762400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:93721800-93747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:93723000-93725400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:93723400-93724400	Enhancers	Liver	Liver
31	chr3:93723600-93724000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:93723600-93725200	Weak transcription	Ovary	ovary
33	chr3:93723600-93726000	Weak transcription	Primary B cells from cord blood	blood
34	chr3:93723600-93726200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:93723600-93726800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:93723600-93727000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:93723600-93728000	Weak transcription	NH-A	brain
38	chr3:93723600-93728200	Weak transcription	Dnd41	blood
39	chr3:93723600-93728600	Weak transcription	NHDF-Ad	bronchial
40	chr3:93723600-93730000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:93723600-93731000	Weak transcription	Fetal Kidney	kidney
42	chr3:93723600-93732800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:93723600-93735400	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:93723600-93743000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:93723600-93743600	Weak transcription	Stomach Mucosa	stomach
46	chr3:93723600-93744600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:93723600-93746600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:93723600-93780800	Weak transcription	Fetal Lung	lung
49	chr3:93723600-93780800	Weak transcription	HSMMtube	muscle
50	chr3:93723800-93724000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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