Variant report

Variant	rs1146646
Chromosome Location	chr1:76265500-76265501
allele	C/T
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
ENSG00000137955	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10732723	1.00[CHB][hapmap]
rs10782558	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	1.00[CHB][hapmap]
rs11161510	0.81[TSI][hapmap]
rs11161511	0.87[TSI][hapmap]
rs11161521	0.81[TSI][hapmap]
rs11161620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161857	1.00[CHB][hapmap]
rs1144336	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs1146581	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs1146588	0.81[EUR][1000 genomes]
rs1146653	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588578	1.00[CHB][hapmap]
rs1159214	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs12021855	0.81[EUR][1000 genomes]
rs12090849	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs12093623	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122939	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123977	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs12127078	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs12136360	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136754	0.80[EUR][1000 genomes]
rs12723575	0.81[EUR][1000 genomes]
rs1565717	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs1770511	0.81[EUR][1000 genomes]
rs1770885	0.81[CEU][hapmap]
rs1770887	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs1858536	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs2029681	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2029683	1.00[CHB][hapmap]
rs2172507	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2172508	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275378	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs2881786	0.81[EUR][1000 genomes]
rs3818855	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs4646961	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs4949677	0.86[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs4949885	1.00[ASN][1000 genomes]
rs5745336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.87[EUR][1000 genomes]
rs5745390	0.87[EUR][1000 genomes]
rs5745427	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs5745433	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap]
rs5745442	1.00[CHB][hapmap]
rs5745449	1.00[CHB][hapmap]
rs61770533	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683437	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6699682	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs7518038	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs7523573	1.00[CHB][hapmap]
rs7534754	0.84[GIH][hapmap];0.84[TSI][hapmap]
rs7547056	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	1.00[CHB][hapmap]
rs931507	1.00[CHB][hapmap];0.91[GIH][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1146646	MSH4	cis	Artery Tibial	GTEx
rs1146646	SNORD45B	cis	parietal	SCAN
rs1146646	MSH4	cis	parietal	SCAN
rs1146646	MSH4	cis	lung	GTEx
rs1146646	MSH4	cis	cerebellum	SCAN
rs1146646	ACADM	cis	cerebellum	SCAN
rs1146646	SNORD45B	cis	cerebellum	SCAN
rs1146646	ACADM	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76257200-76266000	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:76260000-76265800	Weak transcription	Stomach Mucosa	stomach
3	chr1:76262000-76265600	Weak transcription	Small Intestine	intestine
4	chr1:76262400-76266400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:76262400-76267600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:76262400-76267800	Weak transcription	Osteobl	bone
7	chr1:76262400-76269400	Weak transcription	NHDF-Ad	bronchial
8	chr1:76262400-76273200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:76262600-76266000	Weak transcription	Liver	Liver
11	chr1:76262600-76266200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
14	chr1:76262800-76266000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:76262800-76266400	Weak transcription	HSMMtube	muscle
16	chr1:76263000-76265600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:76263000-76269400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:76263000-76276600	Weak transcription	Gastric	stomach
19	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
20	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:76263000-76296200	Weak transcription	Ovary	ovary
22	chr1:76263200-76265600	Weak transcription	Brain Angular Gyrus	brain
23	chr1:76263200-76265600	Weak transcription	NHLF	lung
24	chr1:76263200-76266800	Weak transcription	GM12878-XiMat	blood
25	chr1:76263200-76268000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:76263200-76277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:76263400-76265600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:76263400-76265600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:76263600-76265800	Weak transcription	Fetal Lung	lung
31	chr1:76263600-76284000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:76263800-76266800	Weak transcription	Fetal Brain Female	brain
33	chr1:76264000-76265600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:76264000-76265600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:76264000-76265600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:76264000-76265600	Weak transcription	Pancreas	Pancrea
37	chr1:76264000-76265800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:76264000-76265800	Weak transcription	Brain Anterior Caudate	brain
39	chr1:76264000-76266200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:76264000-76266200	Weak transcription	Lung	lung
41	chr1:76264000-76269400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:76264000-76270600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:76264000-76274200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:76264000-76277000	Weak transcription	HUVEC	blood vessel
45	chr1:76264200-76265800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:76264200-76265800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:76264200-76265800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:76264200-76265800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:76264200-76265800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:76264200-76265800	Weak transcription	Brain Germinal Matrix	brain

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