Variant report

Variant	rs2254715
Chromosome Location	chr9:96363700-96363701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96363030..96364591-chr9:96367019..96369226,2	MCF-7	breast:
2	chr9:96363027..96365894-chr9:96366005..96367741,2	K562	blood:
3	chr9:96353562..96356481-chr9:96362305..96366209,4	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10046907	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10119832	1.00[ASN][1000 genomes]
rs10122014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10512224	0.82[JPT][hapmap]
rs10512226	0.82[JPT][hapmap]
rs10739952	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317260	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13286188	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1331588	0.82[JPT][hapmap]
rs16909211	1.00[CHB][hapmap]
rs1810886	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2250236	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2265573	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274851	1.00[ASN][1000 genomes]
rs2989751	0.82[YRI][hapmap]
rs2994366	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994368	0.86[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3897285	0.82[JPT][hapmap]
rs4146138	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4744257	0.80[YRI][hapmap]
rs55934002	0.92[ASN][1000 genomes]
rs58782393	1.00[ASN][1000 genomes]
rs62573992	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7020195	0.82[JPT][hapmap]
rs7033849	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7038564	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7044283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73651271	1.00[ASN][1000 genomes]
rs7857165	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7869286	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7874126	0.82[JPT][hapmap]
rs914417	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299409	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][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	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:96352400-96384600	Weak transcription	NHLF	lung
5	chr9:96356400-96364000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr9:96356600-96365600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:96357000-96367000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:96357600-96364200	Enhancers	Pancreas	Pancrea
9	chr9:96357600-96364600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:96358400-96364000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr9:96358400-96365200	Enhancers	Primary B cells from peripheral blood	blood
12	chr9:96359200-96364000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr9:96359600-96363800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:96359600-96363800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr9:96359600-96364200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:96359600-96364200	Enhancers	Lung	lung
17	chr9:96359600-96364400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:96359600-96364400	Enhancers	Left Ventricle	heart
19	chr9:96360000-96364000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr9:96360000-96365000	Enhancers	Brain Germinal Matrix	brain
21	chr9:96360200-96364000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:96360400-96364200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr9:96360400-96364400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr9:96360800-96364400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:96361000-96364200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr9:96361000-96364400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:96361000-96369400	Weak transcription	Dnd41	blood
28	chr9:96361200-96364000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:96361200-96364000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr9:96361200-96364200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:96361400-96363800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr9:96361400-96363800	Enhancers	Colon Smooth Muscle	Colon
33	chr9:96361400-96364000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr9:96361400-96372000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:96361400-96380400	Weak transcription	Fetal Brain Male	brain
36	chr9:96361600-96364200	Enhancers	Fetal Muscle Leg	muscle
37	chr9:96361600-96364800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:96361600-96365200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr9:96361600-96379400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:96361800-96363800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr9:96362000-96364200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr9:96362000-96364200	Enhancers	Fetal Muscle Trunk	muscle
43	chr9:96362200-96364000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:96362600-96364200	Enhancers	Right Ventricle	heart
45	chr9:96362800-96364200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr9:96363000-96363800	Weak transcription	Ovary	ovary
47	chr9:96363000-96365200	Weak transcription	Psoas Muscle	Psoas
48	chr9:96363000-96365600	Weak transcription	Right Atrium	heart
49	chr9:96363000-96366200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:96363000-96368600	Weak transcription	Fetal Lung	lung

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