Variant report

Variant	rs123602
Chromosome Location	chr3:52442354-52442355
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52441032..52443343-chr3:52444895..52446688,2	MCF-7	breast:
2	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
3	chr3:52435154..52438907-chr3:52439834..52442973,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163930	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1011064	1.00[JPT][hapmap]
rs1077142	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865972	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11705963	0.92[EUR][1000 genomes]
rs11706001	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706108	0.92[EUR][1000 genomes]
rs11707864	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11709658	0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11711934	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11711974	0.81[LWK][hapmap];0.83[AFR][1000 genomes]
rs11714402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11716017	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11718125	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11721277	0.80[AFR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap]
rs13059674	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs1541495	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052058	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052061	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052068	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016575	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109558	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109559	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2159607	0.93[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28481563	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34261027	0.87[EUR][1000 genomes]
rs34355561	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34523877	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34908451	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35133416	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs352144	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3752819	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs390802	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409803	0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	1.00[JPT][hapmap]
rs4687614	1.00[JPT][hapmap]
rs4687617	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap]
rs498946	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965068	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55997317	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.83[AFR][1000 genomes]
rs56357549	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57441156	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59612757	0.91[EUR][1000 genomes]
rs61150019	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs613519	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs634382	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445386	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs66462821	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67248391	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.88[EUR][1000 genomes]
rs6796333	0.83[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6800707	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs728408	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs758803	1.00[JPT][hapmap]
rs7620015	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7643570	0.91[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs82825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887514	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs887515	0.93[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs123602	ITIH4	cis	multi-tissue	Pritchard
rs123602	DNAH1	cis	cerebellum	SCAN
rs123602	DNAH1	cis	parietal	SCAN
rs123602	SEMA3G	cis	cerebellum	SCAN
rs123602	LOC286359	trans	parietal	SCAN
rs123602	ITIH3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
2	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52420200-52442600	Strong transcription	Fetal Intestine Large	intestine
6	chr3:52430000-52442400	Strong transcription	Brain Substantia Nigra	brain
7	chr3:52430800-52442600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:52430800-52442600	Strong transcription	Brain Cingulate Gyrus	brain
9	chr3:52432000-52442400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:52432200-52442400	Strong transcription	Lung	lung
11	chr3:52432800-52442400	Strong transcription	Thymus	Thymus
12	chr3:52432800-52442400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52433000-52442400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:52433200-52442600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:52433400-52442800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52433800-52442400	Strong transcription	NHLF	lung
17	chr3:52434000-52442800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:52434400-52442800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:52434600-52442600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:52434600-52442600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:52434800-52442800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:52434800-52442800	Strong transcription	Osteobl	bone
23	chr3:52435000-52442400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:52435200-52442600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:52435400-52442400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:52435400-52442400	Strong transcription	Primary hematopoietic stem cells	blood
27	chr3:52435400-52443000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:52435800-52442400	Strong transcription	HepG2	liver
29	chr3:52436000-52442400	Strong transcription	HUVEC	blood vessel
30	chr3:52437000-52442800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:52437400-52443000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:52438000-52443400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:52438200-52443200	Transcr. at gene 5' and 3'	NHEK	skin
34	chr3:52438800-52442400	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:52438800-52442600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr3:52439200-52442400	Strong transcription	HSMMtube	muscle
37	chr3:52439400-52442600	Weak transcription	Psoas Muscle	Psoas
38	chr3:52439600-52442400	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr3:52439600-52442800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:52439600-52443200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:52439800-52442600	Strong transcription	HSMM	muscle
42	chr3:52440200-52442400	Genic enhancers	Duodenum Mucosa	Duodenum
43	chr3:52440200-52442600	Genic enhancers	Gastric	stomach
44	chr3:52440200-52442600	Genic enhancers	Pancreas	Pancrea
45	chr3:52440200-52443000	Weak transcription	Small Intestine	intestine
46	chr3:52440400-52442600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:52440400-52442600	Weak transcription	Primary B cells from cord blood	blood
48	chr3:52440400-52442600	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr3:52440400-52442800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:52440400-52442800	Genic enhancers	HMEC	breast

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