Variant report

Variant	rs2642978
Chromosome Location	chr1:247156066-247156067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247150077..247152155-chr1:247154277..247156770,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10802462	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs10924888	1.00[ASN][1000 genomes]
rs10924899	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs12116484	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs12120876	0.91[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs12135374	1.00[CHD][hapmap]
rs12139893	0.91[CEU][hapmap]
rs12141232	0.88[EUR][1000 genomes]
rs12141355	1.00[CHD][hapmap]
rs12563431	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727420	1.00[ASN][1000 genomes]
rs1573897	1.00[CHD][hapmap]
rs2379189	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642956	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2642957	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642974	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818872	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818874	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540229	0.87[EUR][1000 genomes]
rs28614003	0.86[EUR][1000 genomes]
rs4634944	1.00[CHD][hapmap]
rs4925622	1.00[CHD][hapmap]
rs4925700	1.00[CHD][hapmap]
rs4971320	1.00[ASN][1000 genomes]
rs4971321	1.00[ASN][1000 genomes]
rs4971322	1.00[ASN][1000 genomes]
rs61373194	0.83[EUR][1000 genomes]
rs61852608	0.82[EUR][1000 genomes]
rs61852610	0.88[EUR][1000 genomes]
rs6698643	1.00[CHD][hapmap]
rs7542852	1.00[CHD][hapmap]
rs7543803	0.91[CEU][hapmap]
rs7547915	1.00[CHD][hapmap]
rs7549105	1.00[CHD][hapmap]
rs7550095	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
5	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
6	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
7	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
8	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
9	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
11	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
12	nsv524007	chr1:247098587-247162658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1002054	chr1:247108896-247161897	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv535419	chr1:247108896-247161897	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
17	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
18	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv549546	chr1:247145690-247205056	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2642978	ZNF695	cis	lymphoblastoid	seeQTL
rs2642978	OR2W5	cis	lymphoblastoid	seeQTL
rs2642978	ZNF669	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247136600-247157600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
2	chr1:247136600-247161600	ZNF genes & repeats	Dnd41	blood
3	chr1:247136600-247164600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:247140200-247157800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr1:247140400-247160600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:247140600-247163400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:247140800-247162800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr1:247143600-247159800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
9	chr1:247143800-247157400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:247144200-247163600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:247144800-247159800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr1:247145800-247161400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr1:247146400-247156200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:247146800-247156600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
15	chr1:247150200-247162000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:247151200-247170800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:247151600-247170000	Weak transcription	Osteobl	bone
18	chr1:247154000-247159800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:247154800-247156400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
20	chr1:247154800-247156400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:247154800-247159800	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr1:247155000-247156400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
23	chr1:247155200-247168800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:247155400-247156800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:247155600-247156400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:247155600-247159400	Weak transcription	Thymus	Thymus
27	chr1:247155600-247159800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:247155800-247163200	ZNF genes & repeats	Fetal Brain Female	brain
29	chr1:247156000-247156400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:247156000-247156600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr1:247156000-247156800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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