Variant report

Variant	rs11204912
Chromosome Location	chr1:151877655-151877656
allele	C/G
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	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:
2	chr1:151875998..151878434-chr1:151880509..151883027,2	MCF-7	breast:
3	chr1:151869363..151871176-chr1:151876802..151879330,2	K562	blood:
4	chr1:151869400..151872007-chr1:151876004..151878841,3	K562	blood:
5	chr1:151843538..151846125-chr1:151876423..151878232,2	K562	blood:
6	chr1:151875575..151878356-chr1:151906918..151909478,2	MCF-7	breast:
7	chr1:151877100..151879105-chr1:151904662..151907156,2	K562	blood:
8	chr1:151833014..151835251-chr1:151876525..151878179,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1003107	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10158030	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap]
rs1048910	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10749666	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10788814	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10788816	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10888450	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888453	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11204905	0.95[AMR][1000 genomes]
rs11204911	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204923	1.00[CHB][hapmap]
rs12723616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1352654	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387834	1.00[CHB][hapmap]
rs1387835	1.00[CHB][hapmap]
rs1490187	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs1490190	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1490191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1496037	1.00[CHB][hapmap]
rs1552606	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1552607	1.00[CHB][hapmap]
rs1602245	1.00[CHB][hapmap]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap]
rs1844542	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1873310	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1873311	1.00[CHB][hapmap]
rs1873312	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1967085	1.00[CHB][hapmap]
rs2054948	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2087549	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2130526	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2171917	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338018	1.00[CHB][hapmap]
rs2338200	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2338203	0.89[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338204	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338210	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932563	1.00[CHB][hapmap]
rs2932567	1.00[CHB][hapmap]
rs2932578	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2932584	0.88[ASN][1000 genomes]
rs2932592	1.00[CHB][hapmap]
rs2999514	1.00[CHB][hapmap]
rs2999527	1.00[CHB][hapmap]
rs2999529	1.00[CHB][hapmap]
rs2999535	1.00[CHB][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap]
rs2999538	1.00[CHB][hapmap]
rs2999551	1.00[CHB][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap]
rs2999558	1.00[CHB][hapmap]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap]
rs3007676	1.00[CHB][hapmap]
rs3007679	1.00[CHB][hapmap]
rs3007682	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3007690	1.00[CHB][hapmap]
rs3007692	0.88[ASN][1000 genomes]
rs3007700	1.00[CHB][hapmap]
rs3007701	1.00[CHB][hapmap]
rs3007704	1.00[CHB][hapmap]
rs3122300	1.00[CHB][hapmap]
rs3122301	1.00[CHB][hapmap]
rs34370890	0.91[ASN][1000 genomes]
rs3748805	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3762427	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4551598	0.90[EUR][1000 genomes]
rs4845385	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845388	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845393	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845660	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845699	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587626	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587627	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587628	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587629	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587630	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587641	1.00[CHB][hapmap]
rs6659029	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6662463	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6678664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685291	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690443	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6691350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7529451	1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7532721	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541498	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544380	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7545863	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552869	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902314	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902315	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902316	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959945	1.00[CHB][hapmap]
rs9943225	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11204912	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151841200-151880800	Weak transcription	NHLF	lung
3	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
4	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:151860800-151879800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:151861600-151879800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:151862400-151880400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:151864800-151881400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:151866200-151879600	Weak transcription	NHDF-Ad	bronchial
10	chr1:151866200-151880200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:151866600-151879800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:151867200-151879600	Weak transcription	Fetal Stomach	stomach
13	chr1:151867400-151878600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:151868000-151879800	Weak transcription	Liver	Liver
15	chr1:151868000-151880200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:151868000-151880400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:151868000-151880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:151871400-151878800	Weak transcription	Lung	lung
19	chr1:151871400-151878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:151871400-151879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:151871400-151880400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:151871600-151877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:151871800-151878800	Weak transcription	Thymus	Thymus
24	chr1:151872800-151880800	Weak transcription	Right Atrium	heart
25	chr1:151873000-151880800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:151874400-151878600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:151874800-151880400	Weak transcription	Brain Anterior Caudate	brain
28	chr1:151875000-151879600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:151875000-151879800	Weak transcription	Fetal Lung	lung
30	chr1:151875200-151878200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:151875400-151878400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:151875400-151878400	Weak transcription	Pancreas	Pancrea
33	chr1:151875400-151879600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:151875400-151879600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:151875800-151879600	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:151876400-151879600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:151876600-151878200	Weak transcription	Left Ventricle	heart
38	chr1:151876600-151881400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:151876800-151879200	Enhancers	Fetal Intestine Large	intestine
40	chr1:151877000-151877800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr1:151877000-151877800	Transcr. at gene 5' and 3'	K562	blood
42	chr1:151877000-151878000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:151877000-151878200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:151877000-151878400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:151877000-151878600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:151877000-151880800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:151877200-151877800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr1:151877200-151877800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr1:151877200-151878000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:151877200-151878400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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