Variant report

Variant	rs41444055
Chromosome Location	chr3:99723922-99723923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99723070..99725877-chr3:99978503..99980301,2	MCF-7	breast:
2	chr3:99705385..99708827-chr3:99720207..99724283,4	MCF-7	breast:
3	chr3:99592735..99594887-chr3:99722394..99724729,2	MCF-7	breast:
4	chr3:99652546..99654648-chr3:99721251..99724198,2	MCF-7	breast:
5	chr3:99719980..99722131-chr3:99722963..99725848,2	K562	blood:
6	chr3:99564424..99566018-chr3:99722701..99724331,2	MCF-7	breast:
7	chr3:99723727..99725718-chr3:99976911..99979235,2	K562	blood:
8	chr3:99593399..99595369-chr3:99721874..99725950,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs17313676	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17314245	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17314280	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17314998	1.00[ASW][hapmap]
rs17392822	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17393080	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17584271	1.00[ASW][hapmap]
rs2035400	1.00[YRI][hapmap]
rs41477051	1.00[AFR][1000 genomes]
rs6762809	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6762871	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6764470	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6765822	1.00[AFR][1000 genomes]
rs6772519	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6778756	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6781780	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs6784150	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6787184	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6788807	1.00[YRI][hapmap]
rs6789840	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6790187	0.89[AFR][1000 genomes]
rs6791426	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6794365	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6801514	1.00[YRI][hapmap]
rs6805703	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6805834	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6807137	1.00[YRI][hapmap]
rs6807615	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6808420	1.00[YRI][hapmap]
rs7611313	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[YRI][hapmap]
rs7626214	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7626310	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7637974	1.00[YRI][hapmap]
rs7639304	0.89[AFR][1000 genomes]
rs766777	0.89[AFR][1000 genomes]
rs768527	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][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	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
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99708400-99724600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99714600-99724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:99714800-99724600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:99715800-99724200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:99720200-99727600	Enhancers	Stomach Mucosa	stomach
8	chr3:99720600-99724400	Enhancers	Fetal Intestine Large	intestine
9	chr3:99720800-99724800	Weak transcription	Psoas Muscle	Psoas
10	chr3:99720800-99725000	Enhancers	Fetal Intestine Small	intestine
11	chr3:99721400-99725000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:99721400-99729400	Enhancers	HUVEC	blood vessel
13	chr3:99721600-99724200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr3:99721800-99724400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:99722000-99724200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:99722000-99724400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:99722000-99724600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:99722000-99724600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:99722000-99724600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:99722000-99724600	Weak transcription	Gastric	stomach
21	chr3:99722000-99724600	Weak transcription	Pancreas	Pancrea
22	chr3:99722000-99725800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:99722000-99726200	Weak transcription	Fetal Stomach	stomach
24	chr3:99722000-99726400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:99722000-99726400	Weak transcription	Right Atrium	heart
26	chr3:99722200-99724200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:99722200-99724600	Weak transcription	Fetal Lung	lung
28	chr3:99722200-99724800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:99722200-99724800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:99722200-99725600	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:99722200-99725600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:99722200-99726400	Weak transcription	K562	blood
33	chr3:99722400-99724200	Weak transcription	HSMM	muscle
34	chr3:99722400-99724400	Weak transcription	Right Ventricle	heart
35	chr3:99722400-99724600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:99722400-99724600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:99722400-99724600	Weak transcription	Left Ventricle	heart
38	chr3:99722400-99725200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:99722400-99727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:99722400-99741400	Weak transcription	Aorta	Aorta
41	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:99722600-99724000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:99722600-99724000	Weak transcription	Fetal Kidney	kidney
44	chr3:99722600-99724000	Weak transcription	Osteobl	bone
45	chr3:99722600-99724600	Weak transcription	A549	lung
46	chr3:99722600-99724600	Weak transcription	NH-A	brain
47	chr3:99722600-99724600	Weak transcription	NHDF-Ad	bronchial
48	chr3:99722600-99724800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:99722600-99725200	Weak transcription	NHLF	lung
50	chr3:99722600-99726400	Weak transcription	Fetal Heart	heart

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