Variant report

Variant	rs6445542
Chromosome Location	chr3:52881919-52881920
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52881358..52883021-chr3:52883611..52885400,2	MCF-7	breast:
2	chr3:52875563..52877990-chr3:52881302..52883522,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10049313	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1052728	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486028	1.00[EUR][1000 genomes]
rs13066997	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986739	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991567	1.00[EUR][1000 genomes]
rs2001733	0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001734	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245536	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246888	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246889	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256728	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256734	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276814	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276819	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276821	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276822	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2336155	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336156	1.00[TSI][hapmap]
rs2336157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336158	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336159	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2336546	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2336556	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336557	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336559	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535615	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535616	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535617	0.97[AFR][1000 genomes]
rs2535618	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535619	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535620	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535623	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535628	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535631	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535632	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535636	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535637	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535641	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535642	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535643	0.91[AMR][1000 genomes]
rs2535644	0.91[AMR][1000 genomes]
rs2535645	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564925	1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2577828	1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2581814	1.00[EUR][1000 genomes]
rs2590840	1.00[EUR][1000 genomes]
rs2710315	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710318	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710319	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710320	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710321	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710324	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710325	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710329	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710333	0.88[ASW][hapmap]
rs2710336	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs2710343	1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710344	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878633	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878634	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878635	1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878636	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774361	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687661	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687665	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687666	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687667	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687668	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687670	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687671	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687674	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687675	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687685	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445537	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6791937	1.00[AMR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs7623667	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638431	0.95[AFR][1000 genomes]
rs7645169	0.97[AFR][1000 genomes]
rs7647534	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649515	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9681089	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9877711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6445542	ITIH1	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52866000-52884800	Weak transcription	HMEC	breast
4	chr3:52866200-52885200	Weak transcription	NHEK	skin
5	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
9	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
10	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52873600-52882600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52873600-52889000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:52873800-52882200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:52873800-52889000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52874200-52883800	Enhancers	Psoas Muscle	Psoas
17	chr3:52875800-52882600	Weak transcription	NH-A	brain
18	chr3:52875800-52885800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:52876000-52885800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:52876800-52882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:52876800-52883600	Weak transcription	Aorta	Aorta
22	chr3:52877000-52882200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:52877000-52883200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:52877000-52885000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:52877000-52885600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:52877200-52882200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:52878800-52882000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:52879000-52883000	Weak transcription	Small Intestine	intestine
29	chr3:52879600-52882400	Weak transcription	Colonic Mucosa	Colon
30	chr3:52879600-52882400	Weak transcription	NHDF-Ad	bronchial
31	chr3:52879600-52882800	Weak transcription	Osteobl	bone
32	chr3:52879600-52889800	Weak transcription	K562	blood
33	chr3:52879800-52882400	Weak transcription	Primary B cells from cord blood	blood
34	chr3:52879800-52882400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:52879800-52882600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:52879800-52888200	Weak transcription	Stomach Mucosa	stomach
37	chr3:52879800-52894800	Weak transcription	HSMM	muscle
38	chr3:52880200-52882400	Weak transcription	HSMMtube	muscle
39	chr3:52880200-52883800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:52880200-52885000	Weak transcription	HepG2	liver
41	chr3:52880200-52887200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52880200-52890200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:52880400-52882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:52880400-52882600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:52880400-52883000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:52880400-52884200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:52880400-52890000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr3:52880600-52882400	Weak transcription	NHLF	lung
49	chr3:52880600-52885200	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:52880600-52891000	Weak transcription	Fetal Heart	heart

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