Variant report

Variant	rs12546331
Chromosome Location	chr8:87505968-87505969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87499255..87503133-chr8:87503921..87506529,4	MCF-7	breast:
2	chr8:87502791..87504446-chr8:87504955..87507786,2	MCF-7	breast:
3	chr8:87505860..87508393-chr8:87512519..87515645,3	K562	blood:
4	chr8:87505860..87507671-chr8:87520418..87522186,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176623	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10088389	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10088739	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10092164	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10093238	0.87[CEU][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10093379	0.87[ASN][1000 genomes]
rs10095129	0.89[ASN][1000 genomes]
rs10096443	0.87[CEU][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10956853	0.87[CEU][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1142528	0.87[ASN][1000 genomes]
rs11781016	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13251647	0.89[ASN][1000 genomes]
rs17608967	0.88[CEU][hapmap]
rs1946939	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1946940	0.92[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3883910	0.99[ASN][1000 genomes]
rs4961194	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4961196	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56102132	0.81[ASN][1000 genomes]
rs62510798	0.86[ASN][1000 genomes]
rs62510806	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6415565	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471345	0.87[ASN][1000 genomes]
rs6471349	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471351	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471352	0.88[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471354	0.91[ASN][1000 genomes]
rs6981299	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6988601	0.89[ASN][1000 genomes]
rs6999022	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7006017	0.87[CEU][hapmap]
rs7006629	1.00[CEU][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7015263	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7459811	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7459897	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7460439	0.99[ASN][1000 genomes]
rs7463186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7817738	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7818213	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7820697	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7822494	0.89[ASN][1000 genomes]
rs7823154	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9773093	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv968514	chr8:87495999-87514855	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12546331	RMDN1	cis	Whole Blood	GTEx
rs12546331	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87441800-87507600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:87457400-87507400	Weak transcription	Brain Angular Gyrus	brain
3	chr8:87474000-87517000	Weak transcription	Small Intestine	intestine
4	chr8:87481800-87507400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr8:87481800-87507600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr8:87481800-87507600	Weak transcription	Esophagus	oesophagus
7	chr8:87482000-87507600	Weak transcription	Fetal Brain Male	brain
8	chr8:87482000-87508200	Weak transcription	Fetal Heart	heart
9	chr8:87482000-87508400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr8:87482200-87507600	Weak transcription	Colonic Mucosa	Colon
11	chr8:87482400-87517000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr8:87482800-87506600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:87482800-87519600	Weak transcription	HUVEC	blood vessel
14	chr8:87483000-87508400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:87487600-87507400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr8:87488200-87507400	Weak transcription	Colon Smooth Muscle	Colon
17	chr8:87488200-87507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr8:87488400-87519800	Weak transcription	Psoas Muscle	Psoas
19	chr8:87490400-87507400	Weak transcription	HSMMtube	muscle
20	chr8:87491200-87507600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr8:87493800-87508000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:87494200-87519800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr8:87495200-87506200	Weak transcription	Left Ventricle	heart
24	chr8:87495200-87506400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:87495200-87506800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr8:87495200-87506800	Weak transcription	Fetal Brain Female	brain
27	chr8:87495200-87507200	Weak transcription	Pancreas	Pancrea
28	chr8:87495200-87507400	Weak transcription	Aorta	Aorta
29	chr8:87495200-87507600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr8:87495400-87506400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr8:87495400-87507400	Weak transcription	Brain Hippocampus Middle	brain
32	chr8:87495600-87507600	Weak transcription	HepG2	liver
33	chr8:87495800-87507600	Weak transcription	K562	blood
34	chr8:87496600-87506600	Weak transcription	Lung	lung
35	chr8:87496600-87507400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr8:87496600-87507600	Weak transcription	Brain Substantia Nigra	brain
37	chr8:87496600-87507800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr8:87496600-87515800	Weak transcription	NHLF	lung
39	chr8:87496800-87506600	Weak transcription	Thymus	Thymus
40	chr8:87496800-87507400	Weak transcription	Ovary	ovary
41	chr8:87496800-87507800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr8:87496800-87507800	Weak transcription	Spleen	Spleen
43	chr8:87497000-87506200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:87497000-87516000	Weak transcription	Gastric	stomach
45	chr8:87497000-87516600	Weak transcription	Right Ventricle	heart
46	chr8:87497400-87507000	Weak transcription	Brain Germinal Matrix	brain
47	chr8:87497600-87507800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr8:87497800-87506000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr8:87498000-87507600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr8:87498000-87507800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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