Variant report

Variant	rs965942
Chromosome Location	chr1:227772974-227772975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227753836..227756057-chr1:227770854..227772985,2	K562	blood:
2	chr1:227770918..227773838-chr1:227849267..227851586,2	K562	blood:
3	chr1:227746379..227748088-chr1:227771119..227773064,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10047205	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1021553	0.82[JPT][hapmap]
rs1021554	0.80[JPT][hapmap]
rs10799432	0.87[JPT][hapmap]
rs10799435	0.86[JPT][hapmap]
rs10916165	0.86[JPT][hapmap]
rs10916178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916182	0.87[JPT][hapmap]
rs10916187	0.82[JPT][hapmap]
rs10916192	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12025815	0.87[JPT][hapmap]
rs12059899	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12069550	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12070002	0.87[JPT][hapmap]
rs12070036	0.86[JPT][hapmap]
rs12070539	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12080321	0.87[JPT][hapmap]
rs12080590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12092295	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12095502	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12096675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12132444	0.86[JPT][hapmap]
rs1495846	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1495849	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16847966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16847991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16847992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16848029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923821	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012432	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093609	0.87[JPT][hapmap]
rs2132366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132367	0.87[JPT][hapmap]
rs2256599	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644143	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2644144	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2644146	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2644153	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2644161	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814059	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814060	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814061	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2814084	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2819496	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819498	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2819507	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2819511	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2935146	0.86[JPT][hapmap]
rs2935152	0.91[JPT][hapmap]
rs2935155	0.87[JPT][hapmap]
rs2999745	0.87[JPT][hapmap]
rs2999746	0.87[JPT][hapmap]
rs3010183	0.91[JPT][hapmap]
rs3010186	0.87[JPT][hapmap]
rs3010190	0.91[JPT][hapmap]
rs3010191	0.91[JPT][hapmap]
rs3010192	0.87[JPT][hapmap]
rs3010193	0.87[JPT][hapmap]
rs3010194	0.91[JPT][hapmap]
rs3748806	0.90[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4376731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4589104	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653514	0.86[JPT][hapmap]
rs4653849	0.82[JPT][hapmap]
rs4653853	0.82[JPT][hapmap]
rs58020705	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59034043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59149651	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59753688	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61343450	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66471275	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66491073	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6659745	0.87[EUR][1000 genomes]
rs66736638	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683151	0.87[JPT][hapmap]
rs6688145	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693348	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66938123	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697867	0.82[JPT][hapmap]
rs67216605	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67511833	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67676707	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68046179	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68186506	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72632830	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72632831	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72632832	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72748074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413796	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7528094	0.82[JPT][hapmap]
rs753541	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539151	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903690	0.82[JPT][hapmap]
rs903692	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs903693	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs903694	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs903695	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs965942	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs965942	C1orf35	cis	parietal	SCAN
rs965942	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
2	chr1:227752400-227780600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:227754400-227783600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227760200-227773600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:227760200-227783800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:227760200-227784600	Weak transcription	Fetal Kidney	kidney
7	chr1:227764400-227778400	Weak transcription	HSMMtube	muscle
8	chr1:227766000-227774000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:227766400-227773400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:227767000-227776400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr1:227767200-227773200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:227767200-227776200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:227767200-227779000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:227767600-227774000	Weak transcription	Fetal Stomach	stomach
15	chr1:227767600-227780600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:227767600-227783400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:227768000-227774400	Weak transcription	Gastric	stomach
18	chr1:227768000-227774400	Weak transcription	Ovary	ovary
19	chr1:227768000-227774600	Weak transcription	Right Ventricle	heart
20	chr1:227768000-227783600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:227769800-227773600	Weak transcription	Fetal Brain Male	brain
22	chr1:227769800-227780800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:227770000-227775400	Weak transcription	Placenta	Placenta
24	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:227770400-227775200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:227770600-227781200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:227770600-227784400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:227770800-227774000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:227771200-227773000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr1:227771200-227776200	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr1:227771400-227776200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr1:227771400-227778800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:227771400-227778800	ZNF genes & repeats	Dnd41	blood
34	chr1:227771600-227773400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:227771800-227774400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:227771800-227774600	ZNF genes & repeats	Fetal Lung	lung
37	chr1:227771800-227790600	Weak transcription	Left Ventricle	heart
38	chr1:227772200-227773000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
39	chr1:227772600-227773200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:227772600-227773400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:227772600-227774400	Weak transcription	HSMM	muscle
42	chr1:227772600-227775000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
43	chr1:227772600-227775600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:227772600-227778000	Weak transcription	Primary T cells from cord blood	blood
45	chr1:227772800-227774600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:227772800-227774800	Weak transcription	A549	lung

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