Variant report

Variant	rs236371
Chromosome Location	chr6:36793335-36793336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36792882..36794850-chr6:36817375..36819702,2	MCF-7	breast:
2	chr6:36792218..36793903-chr6:36839226..36841324,2	K562	blood:

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs236363	0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs236364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236375	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs236376	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236388	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5261	chr6:36754545-36798824	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236371	LRFN2	cis	cerebellum	SCAN
rs236371	SCUBE3	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36777000-36797800	Weak transcription	Pancreas	Pancrea
2	chr6:36779000-36794000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:36779400-36797600	Weak transcription	Fetal Brain Female	brain
4	chr6:36781600-36794200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:36787400-36796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:36788400-36802400	Weak transcription	Fetal Kidney	kidney
7	chr6:36788800-36797200	Enhancers	Right Atrium	heart
8	chr6:36789200-36796400	Enhancers	Left Ventricle	heart
9	chr6:36789400-36794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:36789400-36794400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:36789400-36796000	Enhancers	K562	blood
12	chr6:36789600-36794000	Enhancers	HUVEC	blood vessel
13	chr6:36789600-36794600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:36789800-36794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:36789800-36794200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:36789800-36794200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:36789800-36794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:36789800-36802200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:36790000-36794200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:36790000-36794400	Weak transcription	HMEC	breast
21	chr6:36790000-36794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:36790200-36794400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:36790400-36793800	Weak transcription	Brain Anterior Caudate	brain
24	chr6:36790400-36794600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:36790600-36794200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:36790600-36794400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:36790600-36799400	Enhancers	Fetal Muscle Leg	muscle
28	chr6:36790800-36795600	Enhancers	Esophagus	oesophagus
29	chr6:36791000-36795200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:36791200-36794000	Weak transcription	Lung	lung
31	chr6:36791200-36794400	Enhancers	Fetal Muscle Trunk	muscle
32	chr6:36791200-36795000	Weak transcription	Fetal Stomach	stomach
33	chr6:36791200-36805800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:36791400-36796000	Enhancers	Spleen	Spleen
35	chr6:36791400-36798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:36791600-36793400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:36791600-36793400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:36791600-36795000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:36791600-36797000	Enhancers	Right Ventricle	heart
40	chr6:36792000-36795000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:36792000-36796200	Enhancers	Fetal Heart	heart
42	chr6:36792200-36794800	Bivalent Enhancer	HepG2	liver
43	chr6:36792200-36795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:36792400-36794600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:36792400-36794800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:36792400-36796600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:36792800-36794200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:36792800-36796000	Enhancers	Fetal Brain Male	brain
49	chr6:36793000-36793800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:36793000-36794000	Weak transcription	Brain Angular Gyrus	brain

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