Variant report

Variant	rs10002449
Chromosome Location	chr4:99935165-99935166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99934330..99936784-chr4:99941744..99945155,3	MCF-7	breast:
2	chr4:99915686..99917743-chr4:99934020..99937226,3	K562	blood:
3	chr4:99924940..99927322-chr4:99934155..99935780,2	K562	blood:
4	chr4:99915932..99918872-chr4:99933272..99936896,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250496	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000265213	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10084896	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17028370	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28659806	0.96[EUR][1000 genomes]
rs28720156	0.83[AMR][1000 genomes]
rs28730581	0.81[EUR][1000 genomes]
rs28730584	0.81[EUR][1000 genomes]
rs28730596	0.81[EUR][1000 genomes]
rs28730611	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730617	0.81[EUR][1000 genomes]
rs28730625	0.81[EUR][1000 genomes]
rs28730641	0.81[EUR][1000 genomes]
rs28730643	0.81[EUR][1000 genomes]
rs28730644	0.81[EUR][1000 genomes]
rs28730645	0.81[EUR][1000 genomes]
rs28730646	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730649	0.81[EUR][1000 genomes]
rs28894370	0.81[EUR][1000 genomes]
rs28894371	0.83[AMR][1000 genomes]
rs29001228	0.83[AMR][1000 genomes]
rs29001338	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001342	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001346	0.81[EUR][1000 genomes]
rs29001348	0.81[EUR][1000 genomes]
rs5003497	0.81[EUR][1000 genomes]
rs55831712	1.00[EUR][1000 genomes]
rs61431883	0.81[EUR][1000 genomes]
rs62323213	1.00[EUR][1000 genomes]
rs62323214	1.00[EUR][1000 genomes]
rs62323216	1.00[EUR][1000 genomes]
rs62323217	1.00[EUR][1000 genomes]
rs62323230	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323234	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323235	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323240	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323241	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323242	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323245	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62323246	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323247	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323250	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323251	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323253	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323254	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323257	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323258	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323259	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325160	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325189	1.00[EUR][1000 genomes]
rs62325190	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62325192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325196	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325201	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325204	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325206	1.00[EUR][1000 genomes]
rs62325208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325211	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325212	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325213	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325239	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325240	0.81[EUR][1000 genomes]
rs62325241	0.81[EUR][1000 genomes]
rs62325242	0.81[EUR][1000 genomes]
rs62325245	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532781	0.81[EUR][1000 genomes]
rs6532792	0.81[EUR][1000 genomes]
rs6819694	0.81[EUR][1000 genomes]
rs6819724	0.81[EUR][1000 genomes]
rs6822742	0.81[EUR][1000 genomes]
rs6823388	0.81[EUR][1000 genomes]
rs6827292	0.81[EUR][1000 genomes]
rs72897156	0.81[EUR][1000 genomes]
rs7667261	0.81[EUR][1000 genomes]
rs7679102	0.81[EUR][1000 genomes]
rs7681427	0.81[EUR][1000 genomes]
rs7687322	0.81[EUR][1000 genomes]
rs9995869	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10002449	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99918200-99935400	Weak transcription	Ovary	ovary
2	chr4:99918200-99935800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:99918200-99938000	Weak transcription	NHDF-Ad	bronchial
4	chr4:99918600-99937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:99918600-99938600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:99918800-99937800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:99919200-99940000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:99919200-99942000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:99920000-99937800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:99924200-99941600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:99924200-99943600	Weak transcription	Gastric	stomach
12	chr4:99924600-99935400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:99924600-99942000	Weak transcription	Fetal Lung	lung
14	chr4:99925400-99940000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:99925600-99939800	Weak transcription	Thymus	Thymus
16	chr4:99925600-99941200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:99925600-99941200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:99925800-99938800	Weak transcription	Fetal Intestine Large	intestine
19	chr4:99928400-99941400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:99928600-99942400	Weak transcription	Esophagus	oesophagus
21	chr4:99929200-99940600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:99929200-99940800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:99929800-99935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:99930200-99938000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr4:99930600-99941400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:99930600-99941400	Weak transcription	NHEK	skin
27	chr4:99931600-99971400	Weak transcription	Aorta	Aorta
28	chr4:99931800-99940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:99932000-99935600	Weak transcription	K562	blood
30	chr4:99932000-99940200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:99932400-99937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:99932600-99937800	Weak transcription	Dnd41	blood
33	chr4:99932600-99969800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:99933400-99935400	Weak transcription	Primary B cells from cord blood	blood
35	chr4:99933400-99936000	Weak transcription	Fetal Stomach	stomach
36	chr4:99933600-99938200	Weak transcription	Fetal Thymus	thymus
37	chr4:99933800-99935800	Weak transcription	Lung	lung
38	chr4:99933800-99937200	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr4:99934000-99935200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr4:99934000-99935400	Enhancers	HepG2	liver
41	chr4:99934000-99935600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr4:99934000-99938600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr4:99934000-99941600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:99934200-99935400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:99934200-99935800	Weak transcription	Fetal Intestine Small	intestine
46	chr4:99934200-99941600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:99934400-99935200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr4:99934400-99935400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr4:99934400-99935600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr4:99934600-99935400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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