Variant report

Variant	rs35038175
Chromosome Location	chr3:135777678-135777679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSL2-3	chr3:135777567-135777766	l_2481_chr3:135777566-135782085_whiteBloodCell

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10500105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981796	0.83[AMR][1000 genomes]
rs12706650	0.83[AMR][1000 genomes]
rs13307715	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1346368	0.99[ASN][1000 genomes]
rs1427577	0.99[ASN][1000 genomes]
rs1427578	0.99[ASN][1000 genomes]
rs1427581	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17331251	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17390435	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820593	0.88[ASN][1000 genomes]
rs1834827	0.81[EUR][1000 genomes]
rs28667732	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34184477	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34330657	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34574207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35074599	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35275809	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35552657	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35573480	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36103965	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58600715	0.84[ASN][1000 genomes]
rs61518741	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62477097	0.84[ASN][1000 genomes]
rs62481756	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6467001	0.90[ASN][1000 genomes]
rs6467002	0.96[ASN][1000 genomes]
rs6948950	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6958411	0.99[ASN][1000 genomes]
rs6964687	0.99[ASN][1000 genomes]
rs6965492	0.84[ASN][1000 genomes]
rs6970401	0.99[ASN][1000 genomes]
rs6973477	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973838	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780337	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787379	0.87[ASN][1000 genomes]
rs7795867	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804055	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9692521	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:135761600-135783400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:135763000-135785600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:135764400-135790400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:135764600-135778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:135764800-135790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:135765000-135777800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:135765000-135781000	Weak transcription	Fetal Brain Female	brain
11	chr3:135765000-135781200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:135765000-135781200	Weak transcription	Fetal Intestine Small	intestine
13	chr3:135765000-135786000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
15	chr3:135765600-135784200	Weak transcription	Fetal Kidney	kidney
16	chr3:135765600-135785400	Weak transcription	Pancreas	Pancrea
17	chr3:135768800-135800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:135769800-135789400	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:135769800-135789800	Weak transcription	Psoas Muscle	Psoas
20	chr3:135769800-135790000	Weak transcription	Aorta	Aorta
21	chr3:135769800-135790400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:135770000-135787200	Weak transcription	Osteobl	bone
23	chr3:135770000-135789800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:135770000-135800800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:135770400-135789800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:135770800-135781200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:135771200-135802000	Weak transcription	Brain Germinal Matrix	brain
28	chr3:135771200-135809600	Weak transcription	Gastric	stomach
29	chr3:135771400-135778200	Weak transcription	Fetal Lung	lung
30	chr3:135771400-135789000	Weak transcription	HSMMtube	muscle
31	chr3:135772600-135780200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:135772600-135780200	Weak transcription	Fetal Stomach	stomach
33	chr3:135772600-135781000	Weak transcription	Right Ventricle	heart
34	chr3:135772600-135789600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:135772600-135789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:135772600-135789800	Weak transcription	Ovary	ovary
37	chr3:135773000-135787400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:135774400-135802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:135774600-135781000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:135774600-135788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:135774800-135779400	Weak transcription	NH-A	brain
42	chr3:135774800-135789000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:135774800-135789800	Weak transcription	Left Ventricle	heart
44	chr3:135775000-135778400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:135775000-135779400	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:135775000-135781600	Weak transcription	HMEC	breast
47	chr3:135775000-135785000	Weak transcription	HSMM	muscle
48	chr3:135775000-135785200	Weak transcription	NHDF-Ad	bronchial
49	chr3:135775000-135785400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:135775000-135787600	Weak transcription	Rectal Smooth Muscle	rectum

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