Variant report

Variant	rs12415795
Chromosome Location	chr10:97001343-97001344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:96999907-97002082	GM12892	blood:	n/a	n/a
2	POLR2A	chr10:97000935-97001640	GM12891	blood:	n/a	n/a
3	POLR2A	chr10:97000377-97002028	GM12891	blood:	n/a	n/a
4	POLR2A	chr10:97001165-97001549	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:97001035-97001980	GM12891	blood:	n/a	n/a
6	POLR2A	chr10:96999917-97002003	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:97001335-97001405	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:97001246-97001840	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:97000092-97001998	A549	lung:	n/a	n/a
10	POLR2A	chr10:97001175-97001623	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:97001035-97001863	GM12892	blood:	n/a	n/a
12	POLR2A	chr10:97000762-97001513	HepG2	liver:	n/a	n/a
13	POLR2A	chr10:97000411-97001737	GM12892	blood:	n/a	n/a
14	POLR2A	chr10:97000018-97002071	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97001343..97004286-chr10:97048422..97051252,2	K562	blood:

Variant related genes	Relation type
PDLIM1	TF binding region
ENSG00000107438	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10128123	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10218877	0.96[CEU][hapmap]
rs10509683	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10786195	0.85[MEX][hapmap]
rs10882566	0.96[CEU][hapmap]
rs10882568	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10882569	0.88[EUR][1000 genomes]
rs10882572	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs11188223	0.96[CEU][hapmap]
rs11188225	0.96[CEU][hapmap]
rs11188227	0.88[EUR][1000 genomes]
rs11188228	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11188229	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11188230	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs11188238	0.91[EUR][1000 genomes]
rs11188250	0.85[MEX][hapmap]
rs11593722	0.86[AMR][1000 genomes]
rs11596107	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs11596737	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11596853	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599884	0.87[EUR][1000 genomes]
rs11872	0.86[CHB][hapmap]
rs12245722	0.89[EUR][1000 genomes]
rs12262878	0.92[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs12413028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12769820	0.86[EUR][1000 genomes]
rs12776258	0.88[CHB][hapmap]
rs12783947	0.90[EUR][1000 genomes]
rs17110556	0.85[AMR][1000 genomes]
rs17524438	0.92[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs1887182	0.88[CHB][hapmap]
rs2296961	0.85[MEX][hapmap]
rs35999600	0.88[EUR][1000 genomes]
rs4917683	0.88[CHB][hapmap]
rs61871367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695217	0.92[CEU][hapmap]
rs7089314	0.88[CHB][hapmap]
rs7909072	0.92[CEU][hapmap];0.93[CHD][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12415795	PDLIM1	cis	cerebellum	SCAN
rs12415795	PIPSL	cis	cerebellum	SCAN
rs12415795	HELLS	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96990800-97005200	Weak transcription	Psoas Muscle	Psoas
2	chr10:96991000-97001600	Weak transcription	Thymus	Thymus
3	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr10:96991000-97006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:96991000-97006600	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:96991000-97006600	Weak transcription	Right Atrium	heart
8	chr10:96991000-97007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:96991000-97020400	Weak transcription	Fetal Muscle Leg	muscle
10	chr10:96991000-97024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr10:96991400-97019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:96992000-97005000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr10:96992000-97005800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:96992200-97009000	Strong transcription	Liver	Liver
15	chr10:96992400-97006200	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr10:96992600-97004000	Strong transcription	Fetal Intestine Large	intestine
17	chr10:96995200-97002600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:96996200-97001800	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr10:96996200-97004000	Strong transcription	Fetal Intestine Small	intestine
20	chr10:96996200-97006600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr10:96996400-97016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:96996600-97007000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr10:96996800-97002600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:96996800-97005000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr10:96996800-97006600	Weak transcription	HUVEC	blood vessel
26	chr10:96996800-97009400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:96997200-97002000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr10:96997600-97004800	Weak transcription	NH-A	brain
29	chr10:96997600-97006200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:96998000-97005800	Weak transcription	Hela-S3	cervix
31	chr10:96998000-97006400	Weak transcription	NHDF-Ad	bronchial
32	chr10:96998200-97001400	Weak transcription	Fetal Heart	heart
33	chr10:96998200-97005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:96998200-97009400	Weak transcription	Small Intestine	intestine
35	chr10:96998400-97002600	Weak transcription	Stomach Mucosa	stomach
36	chr10:96998400-97003200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr10:96998400-97006200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:96998400-97006400	Weak transcription	HSMM	muscle
39	chr10:96998400-97006600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr10:96998400-97030200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:96999400-97002600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr10:96999600-97008600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:96999800-97002000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:96999800-97002600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr10:96999800-97006600	Strong transcription	Adipose Nuclei	Adipose
46	chr10:96999800-97009000	Strong transcription	Primary B cells from cord blood	blood
47	chr10:97000000-97001400	Strong transcription	Lung	lung
48	chr10:97000000-97001400	Strong transcription	HSMMtube	muscle
49	chr10:97000000-97001400	Strong transcription	Osteobl	bone
50	chr10:97000000-97001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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