Variant report

Variant	rs10788816
Chromosome Location	chr1:151868098-151868099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr1:151867955-151868193	K562	blood:	n/a	n/a
2	MAFK	chr1:151867950-151868283	HepG2	liver:	n/a	n/a
3	MAFF	chr1:151867983-151868205	HepG2	liver:	n/a	n/a
4	MAFK	chr1:151867988-151868260	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151867613..151869663-chr1:151873310..151875520,2	K562	blood:
2	chr1:151867153..151869066-chr1:151941093..151942676,2	MCF-7	breast:
3	chr1:151866512..151869371-chr1:151966159..151968966,3	MCF-7	breast:
4	chr1:151858712..151862714-chr1:151863688..151869439,8	K562	blood:
5	chr1:151848144..151850856-chr1:151866244..151868126,2	MCF-7	breast:
6	chr1:151864758..151867569-chr1:151867706..151869212,2	K562	blood:
7	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:
8	chr1:151862877..151867569-chr1:151867706..151870710,4	K562	blood:

No data

Variant related genes	Relation type
THEM4	TF binding region
ENSG00000229021	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1003107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158030	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1038746	1.00[CHB][hapmap];0.82[AFR][1000 genomes]
rs1038748	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs1048910	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749666	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10788814	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888448	0.83[AMR][1000 genomes]
rs10888449	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888450	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888451	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10888453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204905	0.92[AMR][1000 genomes]
rs11204911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204912	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204923	1.00[CHB][hapmap]
rs12723616	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1352654	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1387834	1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs1387835	1.00[CHB][hapmap]
rs1473493	0.82[AFR][1000 genomes]
rs1473494	0.82[AFR][1000 genomes]
rs1473495	0.82[AFR][1000 genomes]
rs1490187	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs1490190	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1490191	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1496037	1.00[CHB][hapmap]
rs1552605	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs1552606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1552607	1.00[CHB][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs1602245	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1826170	0.82[AFR][1000 genomes]
rs1826171	0.82[AFR][1000 genomes]
rs1844542	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873310	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1873311	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs1873312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967085	1.00[CHB][hapmap]
rs2054948	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087549	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2130526	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171917	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2338018	1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs2338200	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2338203	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2338204	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338210	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932563	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2932567	1.00[CHB][hapmap]
rs2932578	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932588	0.82[AFR][1000 genomes]
rs2932591	0.82[AFR][1000 genomes]
rs2932592	1.00[CHB][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs2932595	0.82[AFR][1000 genomes]
rs2932596	0.82[AFR][1000 genomes]
rs2932597	0.82[AFR][1000 genomes]
rs2999514	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2999518	0.82[AFR][1000 genomes]
rs2999520	0.82[AFR][1000 genomes]
rs2999524	0.82[AFR][1000 genomes]
rs2999525	0.82[AFR][1000 genomes]
rs2999527	1.00[CHB][hapmap];0.82[AFR][1000 genomes]
rs2999529	1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
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];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap]
rs3007676	1.00[CHB][hapmap]
rs3007679	1.00[CHB][hapmap]
rs3007682	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3007690	1.00[CHB][hapmap]
rs3007699	0.82[AFR][1000 genomes]
rs3007700	1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs3007701	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs3007704	1.00[CHB][hapmap]
rs3122300	1.00[CHB][hapmap]
rs3122301	1.00[CHB][hapmap]
rs3748805	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762427	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551598	0.86[EUR][1000 genomes]
rs4845385	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845699	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61113720	0.85[ASN][1000 genomes]
rs6587626	1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587627	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587641	1.00[CHB][hapmap]
rs6659029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6662463	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678664	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6685291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6690443	0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529451	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7532721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7541498	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7544380	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7545863	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552869	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs902315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs902316	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs959945	1.00[CHB][hapmap]
rs971888	0.82[AFR][1000 genomes]
rs9943225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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
rs10788816	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

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	chr1:151844800-151870800	Weak transcription	Gastric	stomach
5	chr1:151844800-151871200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:151845400-151871200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:151846400-151870400	Weak transcription	Right Ventricle	heart
9	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:151847000-151869600	Weak transcription	Small Intestine	intestine
11	chr1:151847000-151871000	Weak transcription	Spleen	Spleen
12	chr1:151847400-151870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:151851000-151871200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:151857000-151873000	Weak transcription	GM12878-XiMat	blood
16	chr1:151857600-151873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:151857600-151874200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:151857800-151868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:151858000-151868400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:151859400-151870800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:151859600-151868400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:151859600-151869200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:151859600-151870600	Weak transcription	HepG2	liver
24	chr1:151860000-151868600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:151860600-151871800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:151860600-151877600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:151860800-151879800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:151861600-151879800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:151862400-151870400	Weak transcription	Psoas Muscle	Psoas
30	chr1:151862400-151880400	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:151863000-151868400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:151863000-151869600	Weak transcription	Colonic Mucosa	Colon
33	chr1:151863200-151870600	Weak transcription	Esophagus	oesophagus
34	chr1:151863600-151868200	Strong transcription	Left Ventricle	heart
35	chr1:151863800-151869000	Weak transcription	Placenta	Placenta
36	chr1:151864000-151868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:151864000-151873000	Weak transcription	Fetal Heart	heart
38	chr1:151864200-151869000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:151864400-151868400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:151864600-151868400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:151864600-151868800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:151864600-151869600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:151864600-151869800	Weak transcription	Fetal Thymus	thymus
44	chr1:151864800-151868200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:151864800-151869000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:151864800-151869400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:151864800-151869600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:151864800-151881400	Weak transcription	Brain Substantia Nigra	brain
49	chr1:151865400-151868200	Strong transcription	Primary T cells from cord blood	blood
50	chr1:151865600-151870600	Weak transcription	Primary hematopoietic stem cells	blood

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