Variant report

Variant	rs6441226
Chromosome Location	chr3:158526223-158526224
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158524631..158526273-chr3:158529876..158531827,2	K562	blood:
2	chr3:158519080..158523533-chr3:158523571..158529220,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118855	Chromatin interaction
ENSG00000272247	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10513528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10936161	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497958	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17643860	0.82[TSI][hapmap]
rs17643917	0.90[YRI][hapmap]
rs28364680	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs41272621	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs41434057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55705231	0.90[EUR][1000 genomes]
rs56261306	0.88[EUR][1000 genomes]
rs56857471	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61796762	0.90[EUR][1000 genomes]
rs61796764	0.90[EUR][1000 genomes]
rs61796766	0.90[EUR][1000 genomes]
rs61796775	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61796802	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7624420	0.89[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7624702	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6441226	LXN	cis	parietal	SCAN
rs6441226	LXN	cis	cerebellum	SCAN
rs6441226	LXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158527400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
3	chr3:158520600-158526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158520600-158527000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:158520600-158543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:158520800-158526400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:158520800-158526400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:158520800-158545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:158521000-158526400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:158521000-158527400	Weak transcription	Fetal Brain Male	brain
11	chr3:158521000-158527400	Weak transcription	Right Ventricle	heart
12	chr3:158521000-158543200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:158521200-158526400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:158521200-158526400	Weak transcription	Thymus	Thymus
15	chr3:158521200-158526400	Weak transcription	NHEK	skin
16	chr3:158521200-158526600	Weak transcription	HSMMtube	muscle
17	chr3:158521200-158527200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:158521200-158527400	Weak transcription	Psoas Muscle	Psoas
19	chr3:158521200-158527600	Weak transcription	Brain Germinal Matrix	brain
20	chr3:158521400-158527400	Weak transcription	Fetal Heart	heart
21	chr3:158521400-158544400	Weak transcription	HepG2	liver
22	chr3:158521600-158526400	Weak transcription	Dnd41	blood
23	chr3:158521800-158526600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:158521800-158527200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:158522200-158533200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:158522400-158526800	Genic enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:158522400-158550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:158522600-158533200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:158522600-158533600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:158522800-158526400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:158522800-158526600	Weak transcription	Hela-S3	cervix
32	chr3:158522800-158527200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:158522800-158532400	Weak transcription	A549	lung
34	chr3:158522800-158533400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:158523000-158533200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:158523000-158544000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:158523200-158526400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:158523200-158526600	Strong transcription	Primary B cells from cord blood	blood
39	chr3:158523400-158526400	Strong transcription	HSMM	muscle
40	chr3:158523400-158533200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:158523400-158533200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:158523400-158533200	Strong transcription	Liver	Liver
43	chr3:158523600-158533200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:158523600-158533200	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:158524000-158529400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:158524200-158527400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:158524600-158533200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:158524800-158533200	Strong transcription	Brain Anterior Caudate	brain
49	chr3:158525000-158526400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:158525000-158527600	Strong transcription	HUVEC	blood vessel

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