Variant report

Variant	rs13196394
Chromosome Location	chr6:71383021-71383022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:71275231..71277384-chr6:71382265..71384787,2	MCF-7	breast:
2	chr6:71377384..71379591-chr6:71381259..71383057,2	MCF-7	breast:
3	chr6:71381415..71384047-chr6:71386712..71389077,2	MCF-7	breast:
4	chr6:71368254..71371028-chr6:71381967..71383874,2	K562	blood:
5	chr6:71375618..71379397-chr6:71381034..71384241,6	K562	blood:

Variant related genes	Relation type
ENSG00000112305	Chromatin interaction
ENSG00000154079	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11752509	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13197338	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13202113	0.93[EUR][1000 genomes]
rs13203355	0.90[EUR][1000 genomes]
rs13212771	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17763077	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34336229	0.90[EUR][1000 genomes]
rs34519120	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35293093	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35528153	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3734371	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3734372	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4706459	0.90[ASN][1000 genomes]
rs4707848	0.88[ASN][1000 genomes]
rs67594983	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9354939	0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs9354940	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs9680	0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription 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	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13196394	PXDN	trans	lymphoblastoid	seeQTL
rs13196394	B3GAT2	cis	cerebellum	SCAN
rs13196394	COL19A1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71378600-71383200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:71378600-71383400	Weak transcription	Aorta	Aorta
3	chr6:71378600-71386600	Weak transcription	Ovary	ovary
4	chr6:71379000-71383600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:71379000-71383600	Enhancers	Small Intestine	intestine
6	chr6:71379200-71383200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:71379200-71383200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:71379200-71384000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:71379200-71386200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:71379400-71383200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:71379400-71383400	Weak transcription	HMEC	breast
12	chr6:71379400-71386000	Weak transcription	Hela-S3	cervix
13	chr6:71379400-71386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:71379400-71388400	Weak transcription	Right Ventricle	heart
15	chr6:71379400-71394600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:71379600-71383200	Weak transcription	NHEK	skin
17	chr6:71379600-71388200	Weak transcription	Primary B cells from cord blood	blood
18	chr6:71380000-71385000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:71380200-71396200	Weak transcription	Brain Angular Gyrus	brain
20	chr6:71380400-71383600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:71381000-71393800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:71381600-71383400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr6:71381600-71386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:71381800-71383400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr6:71381800-71384200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:71382000-71383200	Enhancers	Fetal Heart	heart
27	chr6:71382000-71383200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr6:71382000-71383600	Enhancers	K562	blood
29	chr6:71382000-71384000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr6:71382000-71384200	Enhancers	Psoas Muscle	Psoas
31	chr6:71382200-71383200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:71382200-71383400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:71382200-71383400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr6:71382200-71383600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:71382200-71383600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:71382200-71383800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:71382200-71384000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr6:71382200-71384000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:71382200-71384200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr6:71382400-71383200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr6:71382400-71383200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:71382400-71383200	Enhancers	Liver	Liver
43	chr6:71382400-71383200	Active TSS	GM12878-XiMat	blood
44	chr6:71382400-71383400	Enhancers	Left Ventricle	heart
45	chr6:71382400-71383600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr6:71382400-71384000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:71382400-71384600	Enhancers	Pancreas	Pancrea
48	chr6:71382400-71394600	Weak transcription	Fetal Intestine Small	intestine
49	chr6:71382600-71383200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:71382600-71383200	Enhancers	Adipose Nuclei	Adipose

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