Variant report

Variant	rs2246941
Chromosome Location	chr10:91004916-91004917
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	chr10:91004556..91008070-chr10:91009861..91011850,3	MCF-7	breast:
2	chr10:91003937..91005930-chr10:91020803..91022906,2	K562	blood:

Variant related genes	Relation type
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1051338	0.81[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332327	0.81[CHB][hapmap]
rs1332328	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1332329	0.87[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1412444	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1412445	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243547	0.84[EUR][1000 genomes]
rs2246828	0.81[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246833	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2246942	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2250644	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2250645	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv895882	chr10:91002927-91021645	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2246941	LIPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90977400-91010400	Weak transcription	Fetal Thymus	thymus
2	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:90977600-91008800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:90977600-91009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr10:90977600-91010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:90985200-91010600	Weak transcription	Thymus	Thymus
8	chr10:90987400-91010800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:90987600-91010800	Weak transcription	Pancreas	Pancrea
10	chr10:90987800-91010600	Weak transcription	HSMM	muscle
11	chr10:90988000-91010600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr10:90994800-91010800	Weak transcription	Esophagus	oesophagus
13	chr10:90999600-91005400	Weak transcription	Brain Angular Gyrus	brain
14	chr10:90999600-91010400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:90999800-91010000	Weak transcription	Dnd41	blood
16	chr10:90999800-91010400	Weak transcription	Colon Smooth Muscle	Colon
17	chr10:90999800-91010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:90999800-91010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr10:90999800-91010600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:90999800-91010800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:90999800-91010800	Weak transcription	Ovary	ovary
22	chr10:91000000-91010400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:91000000-91010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:91000200-91010600	Weak transcription	Brain Germinal Matrix	brain
25	chr10:91000200-91010600	Weak transcription	Fetal Brain Female	brain
26	chr10:91000600-91010400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr10:91000600-91010800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr10:91001000-91010600	Weak transcription	Fetal Stomach	stomach
29	chr10:91001000-91010600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr10:91001200-91006400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr10:91001200-91009400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr10:91001200-91010600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:91001200-91010800	Weak transcription	Lung	lung
34	chr10:91002000-91009000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:91002200-91005600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr10:91002200-91010200	Weak transcription	Hela-S3	cervix
37	chr10:91002200-91010400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:91002200-91010400	Weak transcription	Fetal Lung	lung
39	chr10:91002200-91010600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:91002400-91005400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr10:91002400-91005400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:91002400-91008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:91002400-91010200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr10:91002400-91010200	Weak transcription	Fetal Intestine Small	intestine
45	chr10:91002400-91010400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr10:91002400-91010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr10:91002400-91010800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:91002400-91010800	Weak transcription	Left Ventricle	heart
49	chr10:91002600-91007000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr10:91002800-91009400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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