Variant report

Variant	rs340153
Chromosome Location	chr3:111820360-111820361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111816694..111819684-chr3:111820082..111821696,2	MCF-7	breast:
2	chr3:111813838..111815744-chr3:111818709..111820600,2	K562	blood:
3	chr3:111818917..111821397-chr3:111825359..111828351,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs13100905	1.00[CEU][hapmap]
rs1492488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16859217	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16859220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16859233	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16859259	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859301	1.00[CEU][hapmap]
rs16859316	1.00[CEU][hapmap]
rs186866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28722116	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340171	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340175	1.00[ASN][1000 genomes]
rs34879456	0.96[EUR][1000 genomes]
rs4274720	1.00[CEU][hapmap]
rs4682083	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57344127	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59459588	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61645341	0.96[EUR][1000 genomes]
rs6790318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790375	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803848	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7617986	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626450	1.00[CEU][hapmap]
rs7631566	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814494	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9816581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881049	0.96[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	esv2755927	chr3:111794310-111834310	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111806000-111821600	Weak transcription	Lung	lung
2	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
3	chr3:111812000-111825000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:111812000-111844000	Weak transcription	Colonic Mucosa	Colon
5	chr3:111812000-111845600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:111812200-111828000	Weak transcription	Left Ventricle	heart
7	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
8	chr3:111812400-111820400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:111812400-111820600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:111812400-111820800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:111812400-111821400	Weak transcription	Primary B cells from cord blood	blood
12	chr3:111812400-111822000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:111812400-111824800	Weak transcription	Primary T cells from cord blood	blood
14	chr3:111812400-111832000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:111812400-111835800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:111812600-111821800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:111812600-111828000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:111812600-111840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:111814200-111820600	Weak transcription	Pancreas	Pancrea
20	chr3:111814400-111820400	Weak transcription	Fetal Thymus	thymus
21	chr3:111814400-111836000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:111815000-111821800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:111815200-111820400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:111815200-111820800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:111815800-111823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:111816800-111820400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:111816800-111820400	Weak transcription	NHLF	lung
28	chr3:111816800-111820600	Weak transcription	HSMM	muscle
29	chr3:111817000-111820400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:111817000-111820600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:111817000-111822200	Weak transcription	Fetal Intestine Small	intestine
32	chr3:111817000-111822400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:111817000-111828000	Weak transcription	Stomach Mucosa	stomach
34	chr3:111817200-111822200	Weak transcription	Fetal Heart	heart
35	chr3:111817200-111831400	Weak transcription	Hela-S3	cervix
36	chr3:111817200-111833600	Weak transcription	HSMMtube	muscle
37	chr3:111817800-111822400	Weak transcription	Aorta	Aorta
38	chr3:111818800-111820600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:111819000-111840400	Weak transcription	Fetal Stomach	stomach
40	chr3:111819600-111820400	Genic enhancers	NHEK	skin
41	chr3:111819600-111821800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:111819600-111847800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:111819800-111821800	Enhancers	HMEC	breast
44	chr3:111820000-111820600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:111820000-111821400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:111820000-111821600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:111820000-111821600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:111820000-111825200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:111820200-111821000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:111820200-111821200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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