Variant report

Variant	rs942249
Chromosome Location	chr1:46982455-46982456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46981951..46984222-chr1:46986722..46989512,3	MCF-7	breast:
2	chr1:46978731..46981085-chr1:46981137..46983096,2	K562	blood:
3	chr1:46943014..46945161-chr1:46980372..46982820,2	MCF-7	breast:
4	chr1:46974621..46977366-chr1:46981156..46983041,3	K562	blood:
5	chr1:46977403..46980726-chr1:46981041..46983666,4	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1535738	0.92[ASN][1000 genomes]
rs1886115	0.80[AMR][1000 genomes]
rs6429601	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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 target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs942249	KDM4A	cis	parietal	SCAN
rs942249	CLDN19	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46972800-46986000	Weak transcription	Right Atrium	heart
2	chr1:46979400-46982600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:46981200-46984200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:46981600-46984200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:46981800-46982600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr1:46981800-46982600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:46981800-46982600	Enhancers	K562	blood
8	chr1:46981800-46984000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:46981800-46984000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:46981800-46984000	Enhancers	Esophagus	oesophagus
11	chr1:46981800-46984400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:46981800-46986200	Enhancers	A549	lung
13	chr1:46981800-46986800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:46982000-46983200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:46982200-46982600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:46982200-46982600	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr1:46982200-46982600	Enhancers	Gastric	stomach
18	chr1:46982200-46982600	Enhancers	Pancreas	Pancrea
19	chr1:46982200-46982800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr1:46982200-46982800	Enhancers	NHEK	skin
21	chr1:46982200-46983200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:46982200-46983400	Enhancers	HMEC	breast
23	chr1:46982200-46984200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:46982200-46984200	Enhancers	Fetal Intestine Small	intestine
25	chr1:46982200-46984200	Enhancers	Stomach Mucosa	stomach
26	chr1:46982200-46984200	Flanking Active TSS	Hela-S3	cervix
27	chr1:46982400-46982600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:46982400-46982600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:46982400-46982600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
30	chr1:46982400-46982800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:46982400-46982800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:46982400-46982800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr1:46982400-46982800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
34	chr1:46982400-46982800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr1:46982400-46982800	Enhancers	Spleen	Spleen
36	chr1:46982400-46983000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:46982400-46983200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:46982400-46983200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
39	chr1:46982400-46983200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
40	chr1:46982400-46983400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr1:46982400-46983400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:46982400-46983400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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