Variant report

Variant	rs1736890
Chromosome Location	chr6:28189389-28189390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28189386-28190282	K562	blood:	n/a	n/a
2	KAP1	chr6:28189325-28189443	K562	blood:	n/a	n/a

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
2	chr6:28188896..28191056-chr6:28251556..28253787,2	K562	blood:
3	chr6:28188764..28191744-chr6:28301995..28304592,2	MCF-7	breast:
4	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
5	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
6	chr6:28047206..28049069-chr6:28188430..28191262,2	K562	blood:
7	chr6:28081584..28085062-chr6:28187366..28190014,3	K562	blood:
8	chr6:28153153..28155076-chr6:28188462..28190523,2	K562	blood:
9	chr6:28186877..28189778-chr6:28366321..28368559,2	K562	blood:
10	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
11	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
12	chr6:28187375..28189818-chr6:28709219..28712133,2	K562	blood:
13	chr6:28187353..28190192-chr6:28583076..28585455,2	K562	blood:
14	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
15	chr6:27834531..27836106-chr6:28188635..28190287,2	K562	blood:
16	chr6:28188183..28189832-chr6:28247403..28249433,2	MCF-7	breast:
17	chr6:28087049..28089835-chr6:28187380..28190025,2	K562	blood:
18	chr6:28083562..28085258-chr6:28187886..28189759,2	K562	blood:
19	chr6:27857437..27861183-chr6:28187100..28189751,4	K562	blood:
20	chr6:28135337..28137302-chr6:28186822..28190274,4	K562	blood:
21	chr6:28187278..28189645-chr6:28349848..28351599,2	K562	blood:
22	chr6:28187110..28190886-chr6:28224658..28229038,5	K562	blood:
23	chr6:27775362..27779371-chr6:28186093..28189957,4	K562	blood:
24	chr6:28114623..28117122-chr6:28187567..28190304,2	K562	blood:
25	chr6:28187359..28189911-chr6:28455377..28457870,2	K562	blood:
26	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
27	chr6:28188437..28190413-chr6:28337561..28339400,2	K562	blood:
28	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
29	chr6:28130769..28134274-chr6:28187281..28190236,3	K562	blood:
30	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
31	chr6:28163458..28166230-chr6:28188324..28191413,3	K562	blood:
32	chr6:27834298..27836031-chr6:28187958..28190135,2	K562	blood:
33	chr6:27856777..27859583-chr6:28186890..28189718,3	K562	blood:
34	chr6:28188045..28189911-chr6:28456370..28458760,2	K562	blood:
35	chr6:28188391..28191172-chr6:28347437..28349201,2	K562	blood:
36	chr6:28017721..28019447-chr6:28188224..28189953,2	K562	blood:
37	chr6:27860430..27862717-chr6:28186992..28190210,3	K562	blood:

No data

Variant related genes	Relation type
TOB2P1	TF binding region
ZSCAN9	TF binding region
ENSG00000219392	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000184357	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484404	0.90[CEU][hapmap]
rs1062169	0.94[GIH][hapmap];0.83[TSI][hapmap]
rs1150697	0.81[CEU][hapmap]
rs1150698	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150714	0.80[CEU][hapmap]
rs11752073	0.90[CEU][hapmap]
rs11758148	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1233664	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233665	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474589	0.80[CEU][hapmap]
rs16893817	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16893937	0.80[CEU][hapmap]
rs16901846	0.80[CEU][hapmap]
rs1736893	0.83[CHB][hapmap]
rs1736894	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778469	0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778477	0.91[GIH][hapmap]
rs1890809	0.90[CEU][hapmap]
rs2232422	0.80[CEU][hapmap]
rs2281043	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs2622315	0.90[CEU][hapmap]
rs3800325	0.80[CEU][hapmap]
rs6456811	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs6917759	0.90[CEU][hapmap]
rs6923170	0.80[CEU][hapmap]
rs6929559	0.90[CEU][hapmap]
rs73740584	0.93[EUR][1000 genomes]
rs73740587	0.89[EUR][1000 genomes]
rs7744788	0.80[CEU][hapmap]
rs7769054	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs993619	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1736890	AL022393.7	cis	Thyroid	GTEx
rs1736890	ZNF192P1	cis	Adipose Subcutaneous	GTEx
rs1736890	PARD6B	trans	cerebellum	SCAN
rs1736890	ZNF165	cis	parietal	SCAN
rs1736890	HFE	cis	cerebellum	SCAN
rs1736890		cis	Lymphoblastoid	GTEx
rs1736890	ZSCAN23	cis	parietal	SCAN
rs1736890	HIST1H4C	cis	parietal	SCAN
rs1736890	ZNF323	cis	parietal	SCAN
rs1736890	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28186600-28192400	Weak transcription	Spleen	Spleen
2	chr6:28187000-28192400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:28187000-28192400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:28187200-28189800	Weak transcription	NHEK	skin
5	chr6:28187200-28190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:28187200-28192000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28187200-28192000	Weak transcription	HMEC	breast
8	chr6:28187200-28192200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:28187400-28192000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:28187400-28192000	Weak transcription	Hela-S3	cervix
11	chr6:28188200-28191200	Weak transcription	Placenta	Placenta
12	chr6:28188600-28192400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:28188800-28192000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:28188800-28192000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:28189000-28190200	Enhancers	K562	blood

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