Variant report

Variant	rs868351
Chromosome Location	chr1:46009818-46009819
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45986741..45989512-chr1:46009313..46013712,6	MCF-7	breast:
2	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
3	chr1:45998915..46004761-chr1:46006522..46011880,8	K562	blood:
4	chr1:45977514..45980437-chr1:46009344..46010856,2	K562	blood:
5	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
6	chr1:46006129..46009713-chr1:46009736..46013035,4	K562	blood:
7	chr1:46008208..46011176-chr1:46015196..46017542,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117448	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1006216	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs10789464	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10890330	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs11211101	0.82[CHB][hapmap]
rs11211111	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs11211123	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11211124	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211128	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211137	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11211139	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12029322	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12042903	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12046816	0.89[CEU][hapmap]
rs12049503	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12066142	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12077621	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs1771551	0.81[CEU][hapmap]
rs1826691	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2055145	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs2153609	0.82[CHB][hapmap]
rs2185549	0.82[CHB][hapmap]
rs2883968	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34673142	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34768551	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3790582	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs3790583	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4633317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660849	0.82[CHB][hapmap]
rs4660851	0.81[CEU][hapmap]
rs4660852	0.82[CHB][hapmap]
rs4660858	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs4660863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5015340	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518216	0.85[GIH][hapmap]
rs61788336	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788356	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6657284	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[TSI][hapmap]
rs67683090	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs713358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7531253	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs7544178	0.82[CHB][hapmap]
rs7553318	0.82[CHB][hapmap]
rs781226	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs781232	0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9326141	0.82[CHB][hapmap]
rs9429076	0.81[CEU][hapmap]
rs9429160	0.82[CHB][hapmap]
rs9727262	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9729395	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs868351	MUTYH	cis	multi-tissue	Pritchard
rs868351	CYP4Z2P	cis	cerebellum	SCAN
rs868351	GPBP1L1	cis	Lymphoblastoid	GTEx
rs868351	ST3GAL3	cis	parietal	SCAN
rs868351	IPP	cis	lymphoblastoid	seeQTL
rs868351	MAST2	cis	cerebellum	SCAN
rs868351	PRDX1	cis	Thyroid	GTEx
rs868351	TESK2	cis	Whole Blood	GTEx
rs868351	MMACHC	cis	multi-tissue	Pritchard
rs868351	Hs.396207	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46000800-46016000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:46006400-46012200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:46006800-46012200	Enhancers	Fetal Intestine Small	intestine
4	chr1:46007200-46013600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:46007400-46011800	Enhancers	Stomach Mucosa	stomach
6	chr1:46007600-46012000	Enhancers	Fetal Intestine Large	intestine
7	chr1:46008000-46010000	Enhancers	K562	blood
8	chr1:46008000-46010200	Weak transcription	Placenta	Placenta
9	chr1:46008200-46010000	Enhancers	Pancreas	Pancrea
10	chr1:46008200-46010200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr1:46008200-46010400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:46008200-46011000	Enhancers	Spleen	Spleen
13	chr1:46008200-46011400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:46008200-46012200	Enhancers	Fetal Thymus	thymus
15	chr1:46008400-46011400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:46008600-46011600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:46009200-46010000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:46009200-46010000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:46009200-46010000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:46009200-46010000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:46009200-46010000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr1:46009200-46010000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr1:46009200-46010000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:46009200-46010000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:46009200-46010000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr1:46009200-46010000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:46009200-46010000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:46009200-46010000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:46009200-46010000	Enhancers	Gastric	stomach
30	chr1:46009200-46010000	Flanking Active TSS	Dnd41	blood
31	chr1:46009200-46010000	Enhancers	HSMM	muscle
32	chr1:46009200-46010000	Flanking Active TSS	Osteobl	bone
33	chr1:46009200-46010200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:46009200-46010200	Enhancers	Small Intestine	intestine
35	chr1:46009200-46010800	Enhancers	Esophagus	oesophagus
36	chr1:46009200-46011000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:46009200-46011400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:46009200-46011400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:46009200-46011600	Flanking Active TSS	GM12878-XiMat	blood
40	chr1:46009200-46011800	Flanking Active TSS	HepG2	liver
41	chr1:46009400-46010000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr1:46009400-46010000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:46009400-46010000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:46009400-46010000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr1:46009400-46010000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr1:46009400-46010000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr1:46009400-46010000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr1:46009400-46010000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:46009400-46010000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:46009400-46010000	Enhancers	Duodenum Smooth Muscle	Duodenum

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