Variant report

Variant	rs9786978
Chromosome Location	chr1:227968033-227968034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227966135..227968360-chr1:227973552..227975937,2	MCF-7	breast:
2	chr1:227966867..227968420-chr1:228128610..228130112,2	MCF-7	breast:
3	chr1:227967943..227969824-chr1:227975075..227977321,2	K562	blood:
4	chr1:227952215..227955097-chr1:227966264..227970414,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264483	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1056699	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1060295	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799430	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10799439	0.80[EUR][1000 genomes]
rs10799447	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs10799448	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs10916171	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[TSI][hapmap]
rs10916188	0.80[EUR][1000 genomes]
rs10916191	0.80[EUR][1000 genomes]
rs10916203	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916207	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs1111046	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1155807	0.89[CEU][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1810680	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1923823	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2104245	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2236360	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2236361	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4500311	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6426468	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs6426473	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6660432	0.80[EUR][1000 genomes]
rs6693054	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6703846	0.86[ASW][hapmap];0.89[CEU][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs730684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7522634	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526184	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7533588	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7534403	0.89[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7536765	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7539282	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552193	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9969994	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
10	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9786978	ZNF678	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227950800-227974200	Weak transcription	Small Intestine	intestine
2	chr1:227951200-227974400	Weak transcription	Right Atrium	heart
3	chr1:227951800-227970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:227954400-227974600	Weak transcription	HMEC	breast
5	chr1:227955600-227973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227955600-227974000	Weak transcription	Fetal Brain Male	brain
7	chr1:227955800-227972400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227955800-227974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:227955800-227975200	Weak transcription	Hela-S3	cervix
10	chr1:227956000-227974600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:227956600-227973000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:227957000-227968200	Weak transcription	Aorta	Aorta
13	chr1:227957000-227970000	Weak transcription	K562	blood
14	chr1:227957000-227970400	Strong transcription	Fetal Intestine Small	intestine
15	chr1:227957600-227972800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:227957800-227974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:227958000-227975200	Weak transcription	A549	lung
18	chr1:227961200-227969200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:227962000-227974200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:227962400-227973400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:227962400-227974200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:227962600-227970000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:227962600-227973400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:227962800-227970400	Strong transcription	Thymus	Thymus
25	chr1:227962800-227974000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:227963200-227970400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:227963400-227970400	Strong transcription	Primary T cells from cord blood	blood
28	chr1:227963400-227970400	Strong transcription	Pancreas	Pancrea
29	chr1:227963600-227970400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:227963800-227974000	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:227964000-227973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:227964200-227968200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:227964200-227970400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:227964200-227973400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:227964200-227973600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:227964400-227968200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:227964400-227968200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:227964400-227968200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:227964400-227968200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:227964400-227968400	Weak transcription	Brain Anterior Caudate	brain
41	chr1:227964400-227968400	Weak transcription	Right Ventricle	heart
42	chr1:227964400-227972600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:227964400-227973200	Weak transcription	HepG2	liver
44	chr1:227964400-227973400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:227964400-227973800	Weak transcription	Fetal Heart	heart
46	chr1:227964400-227974000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:227964400-227975000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:227964600-227968200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:227964600-227968200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:227964600-227968200	Weak transcription	Fetal Thymus	thymus

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