Variant report

Variant	rs9441828
Chromosome Location	chr1:222720697-222720698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222718086..222720814-chr1:222790387..222793185,3	MCF-7	breast:
2	chr1:222720096..222721859-chr1:222816165..222817680,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1024065	0.87[EUR][1000 genomes]
rs10495194	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs17463740	0.96[EUR][1000 genomes]
rs17464857	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs17511318	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1909194	0.90[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1982983	0.88[EUR][1000 genomes]
rs2006790	0.87[EUR][1000 genomes]
rs2936030	0.88[EUR][1000 genomes]
rs2936039	0.89[EUR][1000 genomes]
rs2936041	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs2936044	0.81[EUR][1000 genomes]
rs2936045	0.81[EUR][1000 genomes]
rs2936046	0.81[EUR][1000 genomes]
rs3002130	0.90[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs3008594	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs3008645	0.82[EUR][1000 genomes]
rs3008647	0.81[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs3008653	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs3008654	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs3008655	0.81[EUR][1000 genomes]
rs35750438	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4328077	0.98[EUR][1000 genomes]
rs73122816	0.92[EUR][1000 genomes]
rs73122823	0.86[EUR][1000 genomes]
rs73122834	0.88[EUR][1000 genomes]
rs73122837	0.88[EUR][1000 genomes]
rs73122849	0.88[EUR][1000 genomes]
rs73122850	0.88[EUR][1000 genomes]
rs73122857	0.89[EUR][1000 genomes]
rs74148133	0.88[EUR][1000 genomes]
rs74148142	0.89[EUR][1000 genomes]
rs9441911	1.00[CHD][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv947385	chr1:222716788-222720718	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv2762168	chr1:222717698-222736854	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9441828	CNIH4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222718400-222721000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:222718800-222722000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:222719400-222721400	Enhancers	HMEC	breast
4	chr1:222719400-222721600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:222719400-222721600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:222719600-222720800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:222719600-222721000	Enhancers	NH-A	brain
8	chr1:222719600-222721000	Flanking Active TSS	Osteobl	bone
9	chr1:222719600-222721200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr1:222719600-222721200	Enhancers	NHEK	skin
11	chr1:222719600-222721400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:222719600-222722000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:222719800-222720800	Enhancers	NHLF	lung
14	chr1:222719800-222721000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:222719800-222721200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:222719800-222721200	Flanking Active TSS	HSMM	muscle
17	chr1:222719800-222721600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:222720000-222720800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:222720000-222720800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:222720000-222720800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:222720000-222720800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr1:222720000-222720800	Flanking Active TSS	Hela-S3	cervix
23	chr1:222720000-222721000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:222720000-222721200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:222720000-222721400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:222720000-222721400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:222720000-222722000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:222720000-222722000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:222720200-222721400	Enhancers	Placenta	Placenta
30	chr1:222720200-222722000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr1:222720200-222722000	Flanking Active TSS	HepG2	liver
32	chr1:222720400-222720800	Active TSS	A549	lung
33	chr1:222720400-222720800	Active TSS	HSMMtube	muscle
34	chr1:222720400-222728800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:222720400-222729200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:222720400-222729200	Weak transcription	Fetal Lung	lung
37	chr1:222720400-222730200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:222720400-222732200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:222720400-222733800	Weak transcription	Fetal Kidney	kidney
40	chr1:222720600-222720800	Flanking Active TSS	NHDF-Ad	bronchial
41	chr1:222720600-222721000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:222720600-222721000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr1:222720600-222721400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:222720600-222721800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:222720600-222729600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:222720600-222730200	Weak transcription	H1 Cell Line	embryonic stem cell

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