Variant report

Variant	rs35590972
Chromosome Location	chr3:99544707-99544708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99535807..99538433-chr3:99542734..99545509,2	MCF-7	breast:
2	chr3:99544479..99546065-chr3:99979068..99981153,2	K562	blood:
3	chr3:99542625..99544746-chr3:99551847..99553962,2	K562	blood:
4	chr3:99534858..99539384-chr3:99540640..99546011,10	K562	blood:
5	chr3:99543572..99547778-chr3:99548143..99551852,5	K562	blood:
6	chr3:99543572..99545458-chr3:99547797..99549652,2	K562	blood:

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1038295	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10804762	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12485299	0.95[AMR][1000 genomes]
rs12486901	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12489030	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12491153	0.93[EUR][1000 genomes]
rs12493124	0.84[EUR][1000 genomes]
rs1492343	0.80[AMR][1000 genomes]
rs1871847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3921767	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4928222	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55874130	0.84[EUR][1000 genomes]
rs55964918	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56140081	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56223679	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56260910	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56335268	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60119031	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61010376	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6792339	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800456	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73858966	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73859911	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73860464	0.95[AMR][1000 genomes]
rs73860470	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7632345	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7635871	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
3	chr3:99537400-99551000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:99537400-99552400	Weak transcription	Ovary	ovary
5	chr3:99537800-99547600	Weak transcription	Aorta	Aorta
6	chr3:99537800-99548200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:99537800-99552400	Weak transcription	Pancreas	Pancrea
8	chr3:99537800-99561800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:99537800-99562400	Weak transcription	Left Ventricle	heart
10	chr3:99538000-99550400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:99538000-99550800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:99538000-99552000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:99538000-99552400	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:99538000-99556000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:99538000-99556800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:99538000-99563600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:99538200-99547200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:99538200-99550800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:99538200-99555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
21	chr3:99538400-99550800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:99538400-99551000	Weak transcription	Primary B cells from cord blood	blood
23	chr3:99540200-99550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:99540800-99552000	Weak transcription	GM12878-XiMat	blood
25	chr3:99541200-99550400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:99542800-99548200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:99542800-99548400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:99543000-99551000	Weak transcription	Small Intestine	intestine
29	chr3:99543000-99557200	Weak transcription	Psoas Muscle	Psoas
30	chr3:99543000-99562600	Weak transcription	Placenta	Placenta
31	chr3:99543200-99544800	Enhancers	NHEK	skin
32	chr3:99543400-99545000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:99543400-99547600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:99543600-99545000	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:99543800-99545000	Enhancers	HSMM	muscle
36	chr3:99543800-99545400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:99544000-99545000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:99544000-99545000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:99544000-99545000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:99544000-99545000	Enhancers	HMEC	breast
41	chr3:99544200-99550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:99544200-99550800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:99544200-99561800	Weak transcription	NHLF	lung
44	chr3:99544200-99564800	Weak transcription	K562	blood
45	chr3:99544400-99545000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:99544400-99549200	Weak transcription	HepG2	liver
47	chr3:99544400-99554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:99544400-99557800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:99544400-99561800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:99544400-99561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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