Variant report

Variant	rs740992
Chromosome Location	chr2:37810532-37810533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37810267..37812004-chr2:37812621..37814787,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10168778	0.90[EUR][1000 genomes]
rs10173816	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181174	0.85[EUR][1000 genomes]
rs10184801	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197948	0.90[EUR][1000 genomes]
rs10208172	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124590	0.83[EUR][1000 genomes]
rs11124592	0.86[EUR][1000 genomes]
rs11687796	0.90[EUR][1000 genomes]
rs11888402	0.81[EUR][1000 genomes]
rs11895388	0.81[EUR][1000 genomes]
rs12615363	0.87[EUR][1000 genomes]
rs13013975	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34752978	0.81[EUR][1000 genomes]
rs35617918	0.84[EUR][1000 genomes]
rs6544093	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6708088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710371	0.87[EUR][1000 genomes]
rs6730320	0.90[EUR][1000 genomes]
rs6733496	0.90[EUR][1000 genomes]
rs6747152	0.90[EUR][1000 genomes]
rs7557304	0.90[EUR][1000 genomes]
rs7560890	0.90[EUR][1000 genomes]
rs7564992	0.86[EUR][1000 genomes]
rs7587009	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs765372	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983895	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833814	chr2:37643132-37840247	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription 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
7	esv2762494	chr2:37802996-37813373	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs740992	PRKD3	cis	cerebellum	SCAN
rs740992	CDC42EP3	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37799200-37812400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:37802000-37812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:37808800-37818000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:37809400-37810800	Enhancers	HUVEC	blood vessel
5	chr2:37809400-37811000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr2:37809400-37814600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:37809400-37814600	Enhancers	Fetal Thymus	thymus
8	chr2:37809400-37817600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:37809600-37810600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr2:37809600-37810600	Enhancers	Fetal Lung	lung
11	chr2:37809600-37810600	Enhancers	NH-A	brain
12	chr2:37809600-37810800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:37809600-37810800	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:37809600-37810800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:37809600-37810800	Enhancers	Thymus	Thymus
16	chr2:37809600-37810800	Flanking Active TSS	NHDF-Ad	bronchial
17	chr2:37809600-37811800	Enhancers	K562	blood
18	chr2:37809600-37813200	Enhancers	HMEC	breast
19	chr2:37809600-37816600	Enhancers	Osteobl	bone
20	chr2:37809800-37810600	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr2:37809800-37810600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:37809800-37810800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:37809800-37810800	Enhancers	Adipose Nuclei	Adipose
24	chr2:37809800-37810800	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:37809800-37811200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:37809800-37811200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:37809800-37811600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr2:37809800-37812400	Enhancers	Fetal Brain Male	brain
29	chr2:37809800-37818400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:37810000-37810600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:37810000-37810800	Flanking Active TSS	HSMMtube	muscle
32	chr2:37810000-37811200	Enhancers	Fetal Brain Female	brain
33	chr2:37810000-37812200	Enhancers	Colon Smooth Muscle	Colon
34	chr2:37810000-37812600	Enhancers	NHEK	skin
35	chr2:37810000-37817400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:37810000-37817600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:37810200-37810600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr2:37810200-37810800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:37810200-37810800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:37810200-37810800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:37810200-37810800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:37810200-37810800	Enhancers	Psoas Muscle	Psoas
43	chr2:37810200-37810800	Enhancers	A549	lung
44	chr2:37810200-37811000	Enhancers	Primary hematopoietic stem cells	blood
45	chr2:37810200-37811000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:37810200-37811400	Enhancers	Fetal Muscle Leg	muscle
47	chr2:37810200-37811400	Enhancers	Gastric	stomach
48	chr2:37810200-37811400	Enhancers	Pancreas	Pancrea
49	chr2:37810200-37811800	Weak transcription	GM12878-XiMat	blood
50	chr2:37810200-37811800	Flanking Active TSS	HSMM	muscle

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