Variant report

Variant	rs2642977
Chromosome Location	chr1:247092378-247092379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247046300..247048217-chr1:247091357..247094558,3	K562	blood:
2	chr1:247092059..247094068-chr1:247274280..247275871,2	K562	blood:
3	chr1:247092146..247096759-chr1:247274350..247278356,6	MCF-7	breast:
4	chr1:247092220..247095330-chr1:247240373..247243272,3	K562	blood:
5	chr1:247090480..247092487-chr1:247093097..247095131,2	MCF-7	breast:
6	chr1:246871057..246874045-chr1:247092351..247094206,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221953	Chromatin interaction
ENSG00000135747	Chromatin interaction
ENSG00000153207	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1039009	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1039010	0.86[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11579381	0.91[JPT][hapmap]
rs11585741	0.82[EUR][1000 genomes]
rs1472275	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1612610	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1613209	0.86[EUR][1000 genomes]
rs1619941	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691240	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1691241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1691242	0.82[AMR][1000 genomes]
rs1691245	0.86[MEX][hapmap]
rs1691246	0.86[MEX][hapmap]
rs1691252	0.80[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1691254	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1691255	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1779958	0.81[MEX][hapmap]
rs1779959	0.81[MEX][hapmap]
rs1779962	0.81[MEX][hapmap]
rs1779964	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1779968	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1779969	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1779985	0.82[ASW][hapmap];0.85[MEX][hapmap]
rs2172796	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2642975	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2642983	0.81[MEX][hapmap]
rs2642991	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800214	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800215	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800219	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800220	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2800221	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2818888	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971278	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs55822102	0.85[AMR][1000 genomes]
rs7542895	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs768197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs903461	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9729306	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9729316	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2642977	ZNF124	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247061200-247093000	Weak transcription	Fetal Brain Male	brain
2	chr1:247069600-247093400	Weak transcription	Colonic Mucosa	Colon
3	chr1:247069600-247093400	Weak transcription	Esophagus	oesophagus
4	chr1:247069800-247093800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:247070000-247093600	Weak transcription	Aorta	Aorta
6	chr1:247070800-247092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:247071000-247093400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:247074200-247093400	Weak transcription	NHLF	lung
9	chr1:247078400-247093600	Weak transcription	Fetal Kidney	kidney
10	chr1:247078600-247093400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:247078800-247093400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:247080400-247093400	Weak transcription	Stomach Mucosa	stomach
13	chr1:247081000-247092400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:247081000-247093400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:247081000-247093400	Weak transcription	HSMMtube	muscle
16	chr1:247081200-247093400	Weak transcription	NH-A	brain
17	chr1:247085400-247093400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:247085600-247093400	Weak transcription	Osteobl	bone
19	chr1:247085800-247093000	Weak transcription	Placenta	Placenta
20	chr1:247085800-247093400	Weak transcription	HUVEC	blood vessel
21	chr1:247086800-247092600	ZNF genes & repeats	GM12878-XiMat	blood
22	chr1:247086800-247093400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:247087000-247092800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:247087000-247092800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:247087200-247092800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:247087200-247093400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:247087200-247093400	Weak transcription	NHDF-Ad	bronchial
28	chr1:247087400-247093400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:247087400-247093400	Weak transcription	Brain Substantia Nigra	brain
30	chr1:247087400-247093400	Weak transcription	Gastric	stomach
31	chr1:247087400-247093400	Weak transcription	Psoas Muscle	Psoas
32	chr1:247087400-247093400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:247087400-247093400	Weak transcription	Right Atrium	heart
34	chr1:247087400-247093400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:247087400-247093400	Weak transcription	Spleen	Spleen
36	chr1:247087400-247093600	Weak transcription	Brain Angular Gyrus	brain
37	chr1:247088200-247092800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:247088400-247092600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:247088600-247093200	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:247088800-247093000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr1:247089000-247093400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:247089000-247093400	Weak transcription	Liver	Liver
43	chr1:247089200-247092600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:247089200-247092800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:247089200-247093000	Weak transcription	Small Intestine	intestine
46	chr1:247089200-247093400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:247089200-247093400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:247089200-247093400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:247089400-247093000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:247089400-247093400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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