Variant report

Variant	rs1146644
Chromosome Location	chr1:76264788-76264789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76259028..76263655-chr1:76264104..76269438,8	MCF-7	breast:
2	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
3	chr1:76263795..76266043-chr1:76279563..76282282,3	K562	blood:
4	chr1:76256951..76259579-chr1:76264447..76268125,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000057468	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1001160	1.00[JPT][hapmap]
rs10873729	0.84[EUR][1000 genomes]
rs10873733	0.82[EUR][1000 genomes]
rs10873797	1.00[JPT][hapmap]
rs11161688	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161718	0.89[EUR][1000 genomes]
rs11161848	1.00[JPT][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163967	1.00[JPT][hapmap]
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	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146635	0.82[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs1146636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146639	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs1146642	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146643	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578480	1.00[JPT][hapmap]
rs11588643	1.00[JPT][hapmap]
rs1159215	1.00[JPT][hapmap]
rs12043473	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12130832	1.00[JPT][hapmap]
rs12131344	1.00[JPT][hapmap]
rs12132750	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142247	1.00[JPT][hapmap]
rs12734931	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463812	0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1498311	1.00[JPT][hapmap]
rs1628063	1.00[JPT][hapmap]
rs1630587	1.00[JPT][hapmap]
rs1689270	1.00[JPT][hapmap]
rs17647178	1.00[JPT][hapmap]
rs1770889	1.00[JPT][hapmap]
rs1796813	1.00[JPT][hapmap]
rs1796815	1.00[JPT][hapmap]
rs1796827	1.00[JPT][hapmap]
rs1856791	1.00[JPT][hapmap]
rs2029682	1.00[JPT][hapmap]
rs211713	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs211719	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs35290302	0.83[GIH][hapmap]
rs3737574	0.83[GIH][hapmap]
rs4638068	1.00[JPT][hapmap]
rs5745323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745325	1.00[JPT][hapmap]
rs5745331	1.00[JPT][hapmap]
rs5745347	1.00[JPT][hapmap]
rs5745383	1.00[JPT][hapmap]
rs5745394	1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs6593520	0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs6593521	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6656501	1.00[JPT][hapmap]
rs721204	1.00[JPT][hapmap]
rs7552289	0.93[GIH][hapmap];0.90[TSI][hapmap]
rs814875	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs814876	0.91[GIH][hapmap];0.83[TSI][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1146644	RABGGTB	cis	parietal	SCAN
rs1146644	MSH4	cis	Artery Tibial	GTEx
rs1146644	RABGGTB	cis	cerebellum	SCAN
rs1146644	MSH4	cis	parietal	SCAN
rs1146644	RABGGTB	cis	lymphoblastoid	seeQTL
rs1146644	MSH4	cis	Esophagus Muscularis	GTEx
rs1146644	MSH4	cis	Muscle Skeletal	GTEx
rs1146644	MSH4	cis	cerebellum	SCAN
rs1146644	ACADM	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
2	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
3	chr1:76256600-76265000	Strong transcription	Primary T cells from cord blood	blood
4	chr1:76256800-76264800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:76256800-76264800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:76256800-76264800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:76257200-76264800	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr1:76257200-76266000	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:76257400-76264800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:76257600-76264800	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:76260000-76265800	Weak transcription	Stomach Mucosa	stomach
12	chr1:76262000-76265600	Weak transcription	Small Intestine	intestine
13	chr1:76262400-76265400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:76262400-76265400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:76262400-76266400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:76262400-76267600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:76262400-76267800	Weak transcription	Osteobl	bone
18	chr1:76262400-76269400	Weak transcription	NHDF-Ad	bronchial
19	chr1:76262400-76273200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:76262600-76265200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:76262600-76265200	Weak transcription	HSMM	muscle
23	chr1:76262600-76265400	Weak transcription	Fetal Brain Male	brain
24	chr1:76262600-76266000	Weak transcription	Liver	Liver
25	chr1:76262600-76266200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
27	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
28	chr1:76262800-76265400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:76262800-76266000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:76262800-76266400	Weak transcription	HSMMtube	muscle
31	chr1:76263000-76265000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:76263000-76265000	Weak transcription	Colonic Mucosa	Colon
33	chr1:76263000-76265200	Weak transcription	Esophagus	oesophagus
34	chr1:76263000-76265400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:76263000-76265600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:76263000-76269400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:76263000-76276600	Weak transcription	Gastric	stomach
38	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
39	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:76263000-76296200	Weak transcription	Ovary	ovary
41	chr1:76263200-76265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:76263200-76265400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:76263200-76265600	Weak transcription	Brain Angular Gyrus	brain
44	chr1:76263200-76265600	Weak transcription	NHLF	lung
45	chr1:76263200-76266800	Weak transcription	GM12878-XiMat	blood
46	chr1:76263200-76268000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:76263200-76277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:76263400-76265600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:76263400-76265600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain

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