Variant report

Variant	rs3789366
Chromosome Location	chr1:180842344-180842345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180840487..180842982-chr1:181055524..181058293,2	K562	blood:
2	chr1:180842169..180845646-chr1:180846177..180849577,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10914096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12085097	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1339768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1970404	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2331626	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2331886	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.96[EUR][1000 genomes]
rs2944259	0.84[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs2944262	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002113	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002115	0.90[EUR][1000 genomes]
rs3002116	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs3002117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3002123	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3013633	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3013634	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3843278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3856058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3897798	0.81[ASN][1000 genomes]
rs4108558	0.99[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs66520411	0.90[EUR][1000 genomes]
rs6659049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659368	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682974	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs67780680	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72707408	0.86[EUR][1000 genomes]
rs72723045	0.90[EUR][1000 genomes]
rs7514404	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7524547	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7541650	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs7548318	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs7550031	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9425881	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv3380465	chr1:180838779-180842477	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789366	MR1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180773400-180849200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:180773800-180853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:180779800-180850800	Weak transcription	Small Intestine	intestine
4	chr1:180796400-180851000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:180803600-180843200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:180804800-180842800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
8	chr1:180812200-180867000	Weak transcription	Ovary	ovary
9	chr1:180819200-180851000	Weak transcription	Fetal Brain Male	brain
10	chr1:180822000-180862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:180822800-180862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:180823000-180854600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:180823400-180843000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:180823600-180847800	Weak transcription	Primary T cells from cord blood	blood
15	chr1:180823600-180860000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:180823800-180851000	Weak transcription	Fetal Kidney	kidney
17	chr1:180823800-180851400	Weak transcription	Pancreas	Pancrea
18	chr1:180823800-180862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:180824000-180848000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:180824000-180867600	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
22	chr1:180824200-180851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:180827800-180856600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:180828000-180852400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:180828000-180853200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:180828000-180853200	Weak transcription	NHEK	skin
27	chr1:180828600-180867800	Weak transcription	HSMM	muscle
28	chr1:180828800-180851000	Weak transcription	Brain Germinal Matrix	brain
29	chr1:180830000-180867600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:180831000-180851400	Weak transcription	Fetal Thymus	thymus
31	chr1:180831200-180858600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:180831600-180847800	Weak transcription	Fetal Brain Female	brain
33	chr1:180831600-180851000	Weak transcription	Brain Angular Gyrus	brain
34	chr1:180831600-180852600	Weak transcription	Fetal Lung	lung
35	chr1:180832200-180848600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:180832400-180842600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:180832400-180842600	Weak transcription	A549	lung
38	chr1:180832400-180844400	Weak transcription	HUVEC	blood vessel
39	chr1:180832400-180848000	Weak transcription	Fetal Heart	heart
40	chr1:180832400-180850000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:180832400-180850000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:180832400-180850800	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:180832400-180850800	Weak transcription	NH-A	brain
44	chr1:180832400-180851000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:180832400-180851000	Weak transcription	Brain Anterior Caudate	brain
46	chr1:180832400-180853200	Weak transcription	Fetal Stomach	stomach
47	chr1:180832600-180854400	Weak transcription	Liver	Liver
48	chr1:180832800-180861800	Weak transcription	HepG2	liver
49	chr1:180833200-180851000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:180833600-180842400	Weak transcription	Dnd41	blood

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