Variant report

Variant	rs4949624
Chromosome Location	chr1:76732617-76732618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11162104	0.84[JPT][hapmap]
rs11162105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069137	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4949625	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs945364	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1499	chr1:76704981-76749688	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4949624	MSH4	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76722000-76732800	Weak transcription	Fetal Kidney	kidney
2	chr1:76723800-76734000	Weak transcription	Brain Anterior Caudate	brain
3	chr1:76724200-76733400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:76726400-76733000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:76726400-76734200	Weak transcription	Thymus	Thymus
6	chr1:76726400-76740000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:76726800-76733400	Weak transcription	Primary B cells from cord blood	blood
8	chr1:76727400-76744800	Weak transcription	Aorta	Aorta
9	chr1:76727600-76733000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:76728600-76732800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:76729200-76734000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:76729800-76734000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:76731000-76733200	Enhancers	Primary T cells from cord blood	blood
14	chr1:76731000-76734000	Weak transcription	Fetal Heart	heart
15	chr1:76731800-76733800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:76731800-76736200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:76731800-76736600	Enhancers	Fetal Thymus	thymus
18	chr1:76732000-76732800	Enhancers	Right Atrium	heart
19	chr1:76732000-76733000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:76732000-76733000	Enhancers	Left Ventricle	heart
21	chr1:76732000-76733400	Enhancers	Fetal Muscle Leg	muscle
22	chr1:76732000-76734000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:76732000-76737000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:76732000-76737600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:76732200-76733200	Enhancers	HSMMtube	muscle
26	chr1:76732200-76733400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:76732200-76736400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:76732200-76736400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:76732200-76737000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:76732400-76732800	Enhancers	Psoas Muscle	Psoas
31	chr1:76732400-76733200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:76732400-76735200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:76732400-76735600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:76732600-76732800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:76732600-76732800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:76732600-76732800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:76732600-76732800	Enhancers	Brain Hippocampus Middle	brain
38	chr1:76732600-76732800	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:76732600-76732800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:76732600-76733400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:76732600-76734400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:76732600-76735000	Enhancers	Dnd41	blood

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