Variant report

Variant	rs3858410
Chromosome Location	chr11:100649197-100649198
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10791427	0.81[ASN][1000 genomes]
rs11224461	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11224474	0.81[ASN][1000 genomes]
rs11823529	0.89[ASN][1000 genomes]
rs12417529	0.81[ASN][1000 genomes]
rs12419467	0.81[ASN][1000 genomes]
rs12419937	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12793858	0.84[ASN][1000 genomes]
rs12801715	0.88[ASN][1000 genomes]
rs17651772	0.89[ASN][1000 genomes]
rs2155140	0.80[ASN][1000 genomes]
rs35472062	0.89[ASN][1000 genomes]
rs35473622	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3858412	0.89[ASN][1000 genomes]
rs4495864	0.81[ASN][1000 genomes]
rs4754698	0.82[ASN][1000 genomes]
rs4754701	0.83[ASN][1000 genomes]
rs486023	0.88[ASN][1000 genomes]
rs492237	0.86[ASN][1000 genomes]
rs536090	0.89[ASN][1000 genomes]
rs582409	0.89[ASN][1000 genomes]
rs588615	0.87[ASN][1000 genomes]
rs595030	0.89[ASN][1000 genomes]
rs600906	0.89[ASN][1000 genomes]
rs607562	0.81[ASN][1000 genomes]
rs607890	0.89[ASN][1000 genomes]
rs612090	0.89[ASN][1000 genomes]
rs614615	0.89[ASN][1000 genomes]
rs626558	0.89[ASN][1000 genomes]
rs6590820	0.81[ASN][1000 genomes]
rs660736	0.89[ASN][1000 genomes]
rs662449	0.89[ASN][1000 genomes]
rs667575	0.86[ASN][1000 genomes]
rs67143028	0.85[ASN][1000 genomes]
rs685611	0.89[ASN][1000 genomes]
rs7125452	0.82[ASN][1000 genomes]
rs9919648	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3858410	ARHGAP42	cis	Artery Tibial	GTEx
rs3858410	TMEM133	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100624600-100655600	Weak transcription	Left Ventricle	heart
2	chr11:100624600-100655600	Weak transcription	Right Ventricle	heart
3	chr11:100633200-100655600	Weak transcription	Psoas Muscle	Psoas
4	chr11:100635400-100649400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr11:100640000-100649600	Weak transcription	Fetal Kidney	kidney
6	chr11:100640000-100655600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:100640200-100651000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:100640400-100651000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:100640800-100655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:100640800-100655200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:100640800-100655600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:100640800-100655600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:100641400-100649600	Weak transcription	Primary B cells from cord blood	blood
14	chr11:100643200-100658000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:100643200-100660000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:100643400-100649200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:100643400-100655600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:100644200-100649200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:100644200-100650000	Enhancers	Stomach Mucosa	stomach
20	chr11:100644400-100649800	Enhancers	Fetal Intestine Small	intestine
21	chr11:100645000-100649200	Enhancers	Fetal Intestine Large	intestine
22	chr11:100645400-100655800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:100645600-100655600	Weak transcription	Gastric	stomach
24	chr11:100645600-100679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:100645800-100655600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr11:100645800-100656000	Weak transcription	Colonic Mucosa	Colon
27	chr11:100645800-100679600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:100646000-100649400	Weak transcription	Fetal Stomach	stomach
29	chr11:100646000-100651000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:100646000-100651200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:100646400-100651200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:100646400-100655800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:100646600-100650200	Weak transcription	Placenta	Placenta
34	chr11:100646800-100649200	Enhancers	HMEC	breast
35	chr11:100647000-100649400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:100647000-100649800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr11:100648000-100649600	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr11:100648400-100649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:100648400-100649400	Enhancers	NHEK	skin
40	chr11:100648600-100649600	Enhancers	Fetal Lung	lung
41	chr11:100648600-100649800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:100648600-100649800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:100648600-100649800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:100648600-100649800	Enhancers	A549	lung
45	chr11:100648800-100649600	Enhancers	HSMMtube	muscle
46	chr11:100648800-100649800	Enhancers	HSMM	muscle
47	chr11:100648800-100654200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:100649000-100649200	Enhancers	Adipose Nuclei	Adipose
49	chr11:100649000-100651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:100649000-100654400	Weak transcription	Fetal Heart	heart

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