Variant report

Variant	rs7200400
Chromosome Location	chr16:81121145-81121146
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	chr16:81109459..81113813-chr16:81119137..81125158,9	MCF-7	breast:
2	chr16:81069395..81071569-chr16:81120451..81122846,2	K562	blood:

Variant related genes	Relation type
ENSG00000166455	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10468366	1.00[MEX][hapmap]
rs11866124	0.85[CHD][hapmap]
rs12444974	0.85[CHD][hapmap]
rs12918103	0.85[CHD][hapmap];0.89[EUR][1000 genomes]
rs12919463	0.89[EUR][1000 genomes]
rs12919980	0.89[EUR][1000 genomes]
rs12921900	0.92[CHD][hapmap];0.89[EUR][1000 genomes]
rs12921990	0.89[EUR][1000 genomes]
rs12922449	0.89[EUR][1000 genomes]
rs12924715	0.89[EUR][1000 genomes]
rs12924719	0.89[EUR][1000 genomes]
rs12928381	0.89[EUR][1000 genomes]
rs12928648	0.92[CHD][hapmap];0.89[EUR][1000 genomes]
rs12928790	0.89[EUR][1000 genomes]
rs12929250	0.92[CHD][hapmap];0.89[EUR][1000 genomes]
rs12930046	0.89[EUR][1000 genomes]
rs12930202	0.85[CHD][hapmap];0.89[EUR][1000 genomes]
rs12931555	0.89[EUR][1000 genomes]
rs12931678	0.89[EUR][1000 genomes]
rs12931766	0.89[EUR][1000 genomes]
rs12931852	0.89[EUR][1000 genomes]
rs12932119	0.89[EUR][1000 genomes]
rs12932272	0.89[EUR][1000 genomes]
rs12932466	0.89[EUR][1000 genomes]
rs12933920	0.89[EUR][1000 genomes]
rs13329702	0.89[EUR][1000 genomes]
rs13333603	0.89[EUR][1000 genomes]
rs13861	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs16954505	0.85[CHD][hapmap]
rs16954525	1.00[MEX][hapmap]
rs2241408	0.89[EUR][1000 genomes]
rs2278021	0.92[CHD][hapmap];0.89[EUR][1000 genomes]
rs2303214	0.85[CHD][hapmap];0.89[EUR][1000 genomes]
rs2549893	0.89[EUR][1000 genomes]
rs28767921	0.82[EUR][1000 genomes]
rs2970077	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs34075739	0.89[EUR][1000 genomes]
rs34082687	0.89[EUR][1000 genomes]
rs34105513	0.89[EUR][1000 genomes]
rs34262209	0.89[EUR][1000 genomes]
rs34270219	0.89[EUR][1000 genomes]
rs34277507	0.89[EUR][1000 genomes]
rs34529307	0.89[EUR][1000 genomes]
rs34545373	0.89[EUR][1000 genomes]
rs34586837	0.89[EUR][1000 genomes]
rs34638844	0.89[EUR][1000 genomes]
rs34699659	0.89[EUR][1000 genomes]
rs34992819	0.89[EUR][1000 genomes]
rs35011155	0.89[EUR][1000 genomes]
rs35110550	0.89[EUR][1000 genomes]
rs35117857	0.89[EUR][1000 genomes]
rs35161190	0.89[EUR][1000 genomes]
rs35282277	0.89[EUR][1000 genomes]
rs35292442	0.89[EUR][1000 genomes]
rs35552248	0.89[EUR][1000 genomes]
rs35674322	0.89[EUR][1000 genomes]
rs35887664	0.89[EUR][1000 genomes]
rs35890164	0.89[EUR][1000 genomes]
rs35899445	0.89[EUR][1000 genomes]
rs36040615	0.89[EUR][1000 genomes]
rs36052656	0.89[EUR][1000 genomes]
rs36056886	0.89[EUR][1000 genomes]
rs36099793	0.89[EUR][1000 genomes]
rs3759931	0.89[EUR][1000 genomes]
rs56064247	0.82[EUR][1000 genomes]
rs57203494	0.89[EUR][1000 genomes]
rs6420421	0.85[CHD][hapmap]
rs71400131	0.89[EUR][1000 genomes]
rs71400134	0.89[EUR][1000 genomes]
rs71400135	0.89[EUR][1000 genomes]
rs71400136	0.89[EUR][1000 genomes]
rs71400137	0.89[EUR][1000 genomes]
rs71400138	0.89[EUR][1000 genomes]
rs71400140	0.89[EUR][1000 genomes]
rs71400141	0.89[EUR][1000 genomes]
rs71400142	0.89[EUR][1000 genomes]
rs7201828	0.82[EUR][1000 genomes]
rs7202326	0.82[EUR][1000 genomes]
rs7202356	0.89[EUR][1000 genomes]
rs7206621	0.82[EUR][1000 genomes]
rs754428	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043855	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs8047325	0.82[EUR][1000 genomes]
rs8047656	0.82[EUR][1000 genomes]
rs8048234	0.85[ASN][1000 genomes]
rs804893	0.89[EUR][1000 genomes]
rs8052980	0.82[EUR][1000 genomes]
rs8057372	0.82[EUR][1000 genomes]
rs8058311	0.82[EUR][1000 genomes]
rs8058907	0.82[EUR][1000 genomes]
rs8061038	1.00[MEX][hapmap]
rs8062810	0.89[EUR][1000 genomes]
rs8063497	0.82[EUR][1000 genomes]
rs8177862	0.89[EUR][1000 genomes]
rs8177863	0.89[EUR][1000 genomes]
rs8177878	0.92[CHD][hapmap];0.89[EUR][1000 genomes]
rs8177879	1.00[GIH][hapmap]
rs8177891	0.89[EUR][1000 genomes]
rs8177919	0.89[EUR][1000 genomes]
rs8177938	0.89[EUR][1000 genomes]
rs874051	0.90[EUR][1000 genomes]
rs9922127	0.82[EUR][1000 genomes]
rs9930427	0.89[EUR][1000 genomes]
rs9932645	0.82[EUR][1000 genomes]
rs9934213	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv978006	chr16:81115953-81121318	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7200400	GCSH	cis	lymphoblastoid	seeQTL
rs7200400	LOC100329108	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81111400-81122400	Weak transcription	Lung	lung
2	chr16:81111400-81122600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr16:81111400-81122800	Weak transcription	Ovary	ovary
4	chr16:81111400-81128200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:81111400-81128400	Weak transcription	Aorta	Aorta
6	chr16:81111400-81128800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr16:81111400-81128800	Weak transcription	Psoas Muscle	Psoas
8	chr16:81111400-81128800	Weak transcription	NHDF-Ad	bronchial
9	chr16:81111400-81129000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:81111400-81129000	Weak transcription	Gastric	stomach
11	chr16:81111400-81129200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:81111600-81122000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr16:81111600-81122200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:81111600-81122400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:81111600-81122400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr16:81111600-81122400	Weak transcription	Fetal Intestine Large	intestine
17	chr16:81111600-81122400	Weak transcription	NHEK	skin
18	chr16:81111600-81122800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr16:81111600-81122800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr16:81111600-81123000	Weak transcription	Primary T cells from cord blood	blood
21	chr16:81111600-81123000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:81111600-81123000	Weak transcription	HMEC	breast
23	chr16:81111600-81123200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr16:81111600-81123200	Weak transcription	Placenta	Placenta
25	chr16:81111600-81125600	Weak transcription	GM12878-XiMat	blood
26	chr16:81111600-81127800	Weak transcription	Brain Substantia Nigra	brain
27	chr16:81111600-81128000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr16:81111600-81128200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:81111600-81128200	Weak transcription	Brain Hippocampus Middle	brain
30	chr16:81111600-81128200	Weak transcription	NH-A	brain
31	chr16:81111600-81128400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr16:81111600-81128400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:81111600-81128400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr16:81111600-81128400	Weak transcription	Brain Anterior Caudate	brain
35	chr16:81111600-81128400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr16:81111600-81128400	Weak transcription	HSMM	muscle
37	chr16:81111600-81128600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr16:81111600-81128600	Weak transcription	Fetal Kidney	kidney
39	chr16:81111600-81128600	Weak transcription	Pancreas	Pancrea
40	chr16:81111600-81128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr16:81111600-81128800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr16:81111600-81128800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr16:81111600-81128800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr16:81111600-81128800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr16:81111600-81128800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:81111600-81128800	Weak transcription	Colon Smooth Muscle	Colon
47	chr16:81111600-81128800	Weak transcription	Fetal Brain Female	brain
48	chr16:81111600-81128800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr16:81111600-81128800	Weak transcription	Right Atrium	heart
50	chr16:81111600-81128800	Weak transcription	Stomach Smooth Muscle	stomach

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