Variant report

Variant	rs6420421
Chromosome Location	chr16:81128206-81128207
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81062101..81064821-chr16:81128185..81130104,2	MCF-7	breast:
2	chr16:81109242..81112738-chr16:81125910..81131139,12	MCF-7	breast:
3	chr16:81109109..81111856-chr16:81126620..81130593,5	MCF-7	breast:
4	chr16:81123255..81125056-chr16:81127455..81129707,2	MCF-7	breast:
5	chr16:81109367..81115509-chr16:81122988..81128884,9	K562	blood:
6	chr16:81128119..81130536-chr16:81138830..81141315,2	K562	blood:
7	chr16:81068173..81071730-chr16:81126382..81131671,6	MCF-7	breast:
8	chr16:81068545..81070561-chr16:81128158..81130238,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261061	Chromatin interaction
ENSG00000252608	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10459871	0.90[CEU][hapmap]
rs10459872	0.90[CEU][hapmap]
rs1048194	0.80[CEU][hapmap]
rs10514512	0.90[CEU][hapmap]
rs10514513	0.90[CEU][hapmap]
rs10514514	0.90[CEU][hapmap]
rs10514515	0.90[CEU][hapmap]
rs11150337	0.81[EUR][1000 genomes]
rs11537	0.90[CEU][hapmap]
rs11866124	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443549	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs12444137	0.90[CEU][hapmap]
rs12444747	0.80[CEU][hapmap]
rs12444974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445303	0.90[CEU][hapmap]
rs12448806	0.83[EUR][1000 genomes]
rs12456	0.80[CEU][hapmap]
rs12918103	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12919980	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12921900	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12921990	0.97[ASN][1000 genomes]
rs12922449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12927239	0.80[CEU][hapmap]
rs12928381	1.00[CHB][hapmap]
rs12928648	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs12928790	0.97[ASN][1000 genomes]
rs12929250	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12930202	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12931678	1.00[CHB][hapmap]
rs12932466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13185	0.81[CEU][hapmap]
rs1414	0.90[CEU][hapmap]
rs1563072	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1563075	0.90[CEU][hapmap]
rs16954505	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs16954513	0.80[CEU][hapmap]
rs16954572	0.90[CEU][hapmap]
rs16954582	0.90[CEU][hapmap]
rs2278021	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs2278022	0.80[CEU][hapmap]
rs2278023	1.00[CHB][hapmap]
rs2278024	0.88[CEU][hapmap]
rs2303214	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2316730	0.80[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2317087	0.83[EUR][1000 genomes]
rs2549891	0.89[CEU][hapmap]
rs2549893	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2549896	0.90[CEU][hapmap]
rs2602402	0.90[CEU][hapmap]
rs2602407	0.90[CEU][hapmap]
rs2970076	0.90[CEU][hapmap]
rs2970077	0.80[CEU][hapmap];0.86[CHD][hapmap];0.85[EUR][1000 genomes]
rs34270219	0.97[ASN][1000 genomes]
rs35161190	0.82[ASN][1000 genomes]
rs35887664	0.84[ASN][1000 genomes]
rs36052656	0.97[ASN][1000 genomes]
rs4324141	0.90[CEU][hapmap]
rs4454990	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs4889225	0.90[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4889229	0.89[EUR][1000 genomes]
rs4889230	0.89[EUR][1000 genomes]
rs4889233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5023849	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5023850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5023852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56198248	0.85[EUR][1000 genomes]
rs56286107	0.83[EUR][1000 genomes]
rs59022620	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60303302	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6420419	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6564819	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7185637	0.90[EUR][1000 genomes]
rs7200400	0.85[CHD][hapmap]
rs7203546	0.89[EUR][1000 genomes]
rs7204040	0.90[CEU][hapmap]
rs7206814	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs73597252	0.88[EUR][1000 genomes]
rs754429	0.90[CEU][hapmap]
rs8043855	0.90[CEU][hapmap];0.93[CHD][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8047495	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs804885	0.90[CEU][hapmap]
rs804895	0.81[CEU][hapmap]
rs804902	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs8050720	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8052415	0.81[EUR][1000 genomes]
rs8052490	0.90[CEU][hapmap]
rs8052694	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8056972	0.90[CEU][hapmap]
rs8059692	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs8177849	0.97[ASN][1000 genomes]
rs8177851	0.85[EUR][1000 genomes]
rs8177862	0.97[ASN][1000 genomes]
rs8177863	0.97[ASN][1000 genomes]
rs8177876	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs8177878	1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[ASN][1000 genomes]
rs8177891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8177919	0.87[ASN][1000 genomes]
rs8177938	0.84[ASN][1000 genomes]
rs8177940	0.85[CEU][hapmap]
rs8177957	0.90[CEU][hapmap]
rs8177959	0.90[CEU][hapmap]
rs874437	0.88[EUR][1000 genomes]
rs935942	0.90[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9923732	0.85[CEU][hapmap]
rs9925940	0.90[CEU][hapmap]
rs9925943	0.90[CEU][hapmap]
rs9926174	0.90[CEU][hapmap]
rs9929586	0.90[CEU][hapmap]
rs9933184	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv530715	chr16:81117168-81252875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv907005	chr16:81121353-81194912	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6420421	ATMIN	cis	Muscle Skeletal	GTEx
rs6420421	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs6420421	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs6420421	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs6420421	LOC100329108	cis	lymphoblastoid	seeQTL
rs6420421	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs6420421	GCSH	cis	multi-tissue	Pritchard
rs6420421	GCSH	cis	lymphoblastoid	seeQTL
rs6420421	GCSH	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81111400-81128400	Weak transcription	Aorta	Aorta
2	chr16:81111400-81128800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:81111400-81128800	Weak transcription	Psoas Muscle	Psoas
4	chr16:81111400-81128800	Weak transcription	NHDF-Ad	bronchial
5	chr16:81111400-81129000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:81111400-81129000	Weak transcription	Gastric	stomach
7	chr16:81111400-81129200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr16:81111600-81128400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:81111600-81128400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:81111600-81128400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:81111600-81128400	Weak transcription	Brain Anterior Caudate	brain
12	chr16:81111600-81128400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr16:81111600-81128400	Weak transcription	HSMM	muscle
14	chr16:81111600-81128600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr16:81111600-81128600	Weak transcription	Fetal Kidney	kidney
16	chr16:81111600-81128600	Weak transcription	Pancreas	Pancrea
17	chr16:81111600-81128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:81111600-81128800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:81111600-81128800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr16:81111600-81128800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr16:81111600-81128800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr16:81111600-81128800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:81111600-81128800	Weak transcription	Colon Smooth Muscle	Colon
24	chr16:81111600-81128800	Weak transcription	Fetal Brain Female	brain
25	chr16:81111600-81128800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr16:81111600-81128800	Weak transcription	Right Atrium	heart
27	chr16:81111600-81128800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:81111600-81128800	Weak transcription	HSMMtube	muscle
29	chr16:81111600-81128800	Weak transcription	Osteobl	bone
30	chr16:81111600-81129000	Weak transcription	Brain Germinal Matrix	brain
31	chr16:81111600-81129000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr16:81111600-81129200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:81111600-81129200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr16:81111600-81129200	Weak transcription	Left Ventricle	heart
35	chr16:81111800-81128800	Weak transcription	Fetal Brain Male	brain
36	chr16:81111800-81128800	Weak transcription	Fetal Thymus	thymus
37	chr16:81114000-81128400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr16:81120800-81128600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr16:81122000-81129400	Weak transcription	Small Intestine	intestine
40	chr16:81123000-81128400	Weak transcription	Fetal Heart	heart
41	chr16:81123200-81128800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr16:81123200-81129200	Weak transcription	Lung	lung
43	chr16:81123400-81128400	Weak transcription	Adipose Nuclei	Adipose
44	chr16:81123400-81128400	Weak transcription	Fetal Lung	lung
45	chr16:81123400-81128600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr16:81123400-81128600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:81123400-81128600	Weak transcription	Fetal Intestine Large	intestine
48	chr16:81123400-81128800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:81123600-81128400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr16:81123600-81128400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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