Variant report

Variant	rs1146643
Chromosome Location	chr1:76263558-76263559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76262752..76264685-chr6:26156867..26159856,2	K562	blood:
2	chr1:76213109..76217378-chr1:76260068..76263795,4	K562	blood:
3	chr1:76262942..76264627-chr1:76319779..76321493,2	K562	blood:
4	chr1:76208992..76212319-chr1:76261590..76264096,3	K562	blood:
5	chr1:76257416..76260329-chr1:76260481..76263578,4	MCF-7	breast:
6	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
7	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:

Variant related genes	Relation type
ENSG00000181227	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10873729	0.84[EUR][1000 genomes]
rs10873733	0.82[EUR][1000 genomes]
rs11161688	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161718	0.89[EUR][1000 genomes]
rs1144340	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146607	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1146609	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1146610	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1146630	0.80[AMR][1000 genomes]
rs1146631	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146634	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146636	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146637	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146639	0.81[AMR][1000 genomes]
rs1146642	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146644	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734931	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745323	0.92[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1146643	MSH4	cis	Muscle Skeletal	GTEx
rs1146643	MSH4	cis	Esophagus Muscularis	GTEx
rs1146643	MSH4	cis	Artery Tibial	GTEx
rs1146643	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
2	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
3	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
4	chr1:76255600-76264000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr1:76255800-76264000	Strong transcription	Brain Anterior Caudate	brain
6	chr1:76255800-76264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:76255800-76264200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:76255800-76264400	Strong transcription	Fetal Muscle Leg	muscle
9	chr1:76256000-76264200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:76256000-76264200	Strong transcription	Fetal Thymus	thymus
11	chr1:76256000-76264400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:76256000-76264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:76256000-76264600	Strong transcription	Fetal Stomach	stomach
14	chr1:76256400-76264400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:76256600-76264000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr1:76256600-76264000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:76256600-76264200	Strong transcription	Brain Cingulate Gyrus	brain
18	chr1:76256600-76264600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:76256600-76265000	Strong transcription	Primary T cells from cord blood	blood
20	chr1:76256800-76264000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:76256800-76264200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:76256800-76264200	Strong transcription	Fetal Intestine Large	intestine
23	chr1:76256800-76264200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:76256800-76264400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:76256800-76264600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:76256800-76264800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:76256800-76264800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:76256800-76264800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:76257000-76264200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:76257200-76264800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr1:76257200-76266000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:76257400-76264200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:76257400-76264800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:76257600-76263600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:76257600-76264200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:76257600-76264600	Strong transcription	Left Ventricle	heart
37	chr1:76257600-76264800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:76258000-76264200	Strong transcription	NH-A	brain
39	chr1:76258200-76264000	Strong transcription	HUVEC	blood vessel
40	chr1:76258400-76264000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:76260000-76264000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:76260000-76264600	Strong transcription	Spleen	Spleen
43	chr1:76260000-76265800	Weak transcription	Stomach Mucosa	stomach
44	chr1:76260200-76264200	Strong transcription	Thymus	Thymus
45	chr1:76260400-76263800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:76260800-76264000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:76261000-76263600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:76261000-76264000	Strong transcription	Fetal Intestine Small	intestine
49	chr1:76261000-76264000	Strong transcription	Lung	lung
50	chr1:76261000-76264000	Strong transcription	Pancreas	Pancrea

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