Variant report

Variant	rs10004678
Chromosome Location	chr4:22490444-22490445
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22488399..22490950-chr4:22493521..22495053,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10000829	1.00[EUR][1000 genomes]
rs10006549	1.00[EUR][1000 genomes]
rs10012247	1.00[EUR][1000 genomes]
rs10013414	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10013902	1.00[EUR][1000 genomes]
rs10017087	1.00[EUR][1000 genomes]
rs10019604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10021864	1.00[EUR][1000 genomes]
rs10029008	1.00[EUR][1000 genomes]
rs10029089	1.00[EUR][1000 genomes]
rs10029265	1.00[EUR][1000 genomes]
rs10938900	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11944057	1.00[EUR][1000 genomes]
rs28414141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28426972	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28490882	1.00[EUR][1000 genomes]
rs28501220	1.00[EUR][1000 genomes]
rs28518171	1.00[EUR][1000 genomes]
rs28521540	1.00[EUR][1000 genomes]
rs28542982	1.00[EUR][1000 genomes]
rs28591328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645358	1.00[EUR][1000 genomes]
rs28660699	1.00[EUR][1000 genomes]
rs28667991	1.00[EUR][1000 genomes]
rs28698249	1.00[EUR][1000 genomes]
rs28703830	1.00[EUR][1000 genomes]
rs28729399	1.00[EUR][1000 genomes]
rs28775576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28787887	1.00[EUR][1000 genomes]
rs28798753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28839846	1.00[EUR][1000 genomes]
rs28882371	1.00[EUR][1000 genomes]
rs34198330	1.00[EUR][1000 genomes]
rs59046669	1.00[EUR][1000 genomes]
rs6448148	1.00[EUR][1000 genomes]
rs6836362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840912	1.00[EUR][1000 genomes]
rs6846776	1.00[EUR][1000 genomes]
rs73123531	1.00[EUR][1000 genomes]
rs73123532	1.00[EUR][1000 genomes]
rs73123536	1.00[EUR][1000 genomes]
rs7657782	1.00[EUR][1000 genomes]
rs7662891	1.00[EUR][1000 genomes]
rs9654097	1.00[EUR][1000 genomes]
rs980589	1.00[EUR][1000 genomes]
rs9992606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9993875	1.00[EUR][1000 genomes]
rs9995752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:22462000-22493200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:22484800-22492400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:22484800-22493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:22484800-22498400	Weak transcription	Gastric	stomach
6	chr4:22485000-22492400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:22485000-22506000	Weak transcription	Esophagus	oesophagus
8	chr4:22485400-22492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:22485600-22492400	Weak transcription	Liver	Liver
10	chr4:22485600-22493200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:22485600-22501400	Weak transcription	Hela-S3	cervix
12	chr4:22485600-22502000	Weak transcription	A549	lung
13	chr4:22485800-22491600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:22486400-22500600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:22486600-22492200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:22486600-22492200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:22486600-22492400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:22486800-22492400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:22487800-22490600	Enhancers	HepG2	liver
20	chr4:22487800-22492400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:22488000-22494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:22488200-22491400	Weak transcription	Aorta	Aorta
23	chr4:22488400-22503000	Weak transcription	Small Intestine	intestine
24	chr4:22488600-22516000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:22488800-22496800	Weak transcription	HMEC	breast
26	chr4:22488800-22497800	Weak transcription	NHEK	skin
27	chr4:22488800-22503600	Weak transcription	NHLF	lung
28	chr4:22489200-22492400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:22489200-22492400	Weak transcription	Brain Anterior Caudate	brain
30	chr4:22489200-22492400	Weak transcription	Ovary	ovary
31	chr4:22489400-22490800	Weak transcription	Fetal Intestine Small	intestine
32	chr4:22489400-22492400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:22489400-22492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:22489400-22492400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:22489400-22492400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:22489400-22492400	Weak transcription	HSMMtube	muscle
37	chr4:22489400-22493200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:22489400-22496800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:22489400-22496800	Weak transcription	Fetal Stomach	stomach
40	chr4:22489400-22500600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:22489600-22492200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr4:22489600-22492400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:22489600-22503800	Weak transcription	HSMM	muscle
44	chr4:22489800-22492200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:22490000-22492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:22490200-22490600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:22490200-22491400	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:22490200-22491400	Weak transcription	Fetal Heart	heart
49	chr4:22490200-22492400	Weak transcription	Lung	lung
50	chr4:22490200-22492400	Weak transcription	Pancreas	Pancrea

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