Variant report

Variant	rs2288096
Chromosome Location	chr3:120409526-120409527
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120406419..120409773-chr3:120409851..120413198,4	MCF-7	breast:
2	chr3:120396266..120398930-chr3:120408649..120411497,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10934532	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12489104	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292719	0.81[TSI][hapmap];0.82[YRI][hapmap]
rs6796222	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs72625420	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429748	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7430785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7620570	1.00[YRI][hapmap]
rs7633399	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs9814744	1.00[YRI][hapmap]
rs9838458	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs9854081	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs9985346	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120397600-120421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:120397800-120410600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:120397800-120410600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:120397800-120412200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:120397800-120415800	Weak transcription	Ovary	ovary
6	chr3:120397800-120420600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:120397800-120421800	Weak transcription	Aorta	Aorta
8	chr3:120397800-120424800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:120398200-120410400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:120398200-120412200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:120398200-120412200	Weak transcription	HMEC	breast
12	chr3:120398200-120415200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:120398200-120423200	Weak transcription	Psoas Muscle	Psoas
14	chr3:120398200-120427000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:120398200-120427800	Weak transcription	Placenta	Placenta
16	chr3:120398200-120430200	Weak transcription	NHEK	skin
17	chr3:120398200-120438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:120398400-120412200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:120398400-120412400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:120398600-120411800	Weak transcription	HUVEC	blood vessel
21	chr3:120398800-120442200	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:120400000-120410600	Weak transcription	Hela-S3	cervix
23	chr3:120400000-120412200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:120400200-120421600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:120401000-120424800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:120401200-120411200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:120402200-120411800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:120402200-120412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:120402400-120423600	Weak transcription	Lung	lung
30	chr3:120402600-120410400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:120402600-120420800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:120402800-120412200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:120402800-120421800	Weak transcription	Fetal Kidney	kidney
34	chr3:120402800-120456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:120403200-120412000	Weak transcription	Fetal Intestine Small	intestine
36	chr3:120403600-120423800	Weak transcription	Spleen	Spleen
37	chr3:120404000-120415600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:120404000-120423600	Weak transcription	Pancreas	Pancrea
39	chr3:120404200-120416000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:120404800-120421800	Weak transcription	HSMM	muscle
41	chr3:120405000-120412400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:120405600-120436800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:120406000-120412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:120406000-120415400	Weak transcription	Left Ventricle	heart
45	chr3:120406000-120421800	Weak transcription	Dnd41	blood
46	chr3:120406400-120415200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:120406400-120436600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:120406600-120421800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:120406800-120421200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:120407000-120417600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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