Variant report

Variant	rs4288197
Chromosome Location	chr6:56398019-56398020
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56396433..56398982-chr6:56400861..56403143,2	MCF-7	breast:
2	chr6:56390066..56391904-chr6:56396984..56399522,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1024196	0.84[EUR][1000 genomes]
rs11963288	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11966986	0.84[EUR][1000 genomes]
rs11967796	0.84[EUR][1000 genomes]
rs11970410	0.84[EUR][1000 genomes]
rs12662511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1407831	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1535609	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1535611	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16887928	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16887983	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs16888070	0.84[EUR][1000 genomes]
rs16888106	0.84[EUR][1000 genomes]
rs17757606	0.95[ASN][1000 genomes]
rs17757660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17830661	0.95[ASN][1000 genomes]
rs17830685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17830715	0.98[ASN][1000 genomes]
rs17830726	0.98[ASN][1000 genomes]
rs17830810	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2144407	0.84[EUR][1000 genomes]
rs2180148	0.84[EUR][1000 genomes]
rs2207678	0.84[EUR][1000 genomes]
rs2397224	0.84[EUR][1000 genomes]
rs28633631	0.84[EUR][1000 genomes]
rs3800026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924307	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41267673	0.84[EUR][1000 genomes]
rs41271848	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41271850	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41271854	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41271856	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41271872	0.84[EUR][1000 genomes]
rs41271876	0.84[EUR][1000 genomes]
rs41271878	0.84[EUR][1000 genomes]
rs4256439	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45442999	0.89[EUR][1000 genomes]
rs57289287	0.84[EUR][1000 genomes]
rs57350484	0.84[EUR][1000 genomes]
rs57790896	0.84[EUR][1000 genomes]
rs57822928	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58565063	0.84[EUR][1000 genomes]
rs58730144	0.89[EUR][1000 genomes]
rs59772940	0.84[EUR][1000 genomes]
rs59864125	0.89[EUR][1000 genomes]
rs62621210	0.89[EUR][1000 genomes]
rs6459167	0.84[EUR][1000 genomes]
rs6459168	0.84[EUR][1000 genomes]
rs6900572	0.84[EUR][1000 genomes]
rs6903815	0.84[EUR][1000 genomes]
rs6941626	0.84[EUR][1000 genomes]
rs73455767	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73455782	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73465854	0.89[EUR][1000 genomes]
rs73746926	0.84[EUR][1000 genomes]
rs73746929	0.84[EUR][1000 genomes]
rs73747826	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73747832	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73749935	0.89[EUR][1000 genomes]
rs73749942	0.89[EUR][1000 genomes]
rs73749948	0.89[EUR][1000 genomes]
rs73749949	0.89[EUR][1000 genomes]
rs7749100	0.84[EUR][1000 genomes]
rs7759479	0.84[EUR][1000 genomes]
rs7760503	0.84[EUR][1000 genomes]
rs7760515	0.84[EUR][1000 genomes]
rs7760542	0.84[EUR][1000 genomes]
rs7760701	0.84[EUR][1000 genomes]
rs7761027	0.84[EUR][1000 genomes]
rs7769014	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7775134	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56362800-56400200	Weak transcription	Colonic Mucosa	Colon
3	chr6:56363000-56402200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:56374600-56399600	Weak transcription	Fetal Thymus	thymus
5	chr6:56376400-56407200	Weak transcription	Gastric	stomach
6	chr6:56377200-56404200	Weak transcription	K562	blood
7	chr6:56380600-56401200	Weak transcription	Psoas Muscle	Psoas
8	chr6:56383200-56402400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:56384400-56402200	Weak transcription	Small Intestine	intestine
10	chr6:56388000-56402200	Strong transcription	Fetal Intestine Large	intestine
11	chr6:56388200-56401800	Strong transcription	Liver	Liver
12	chr6:56388800-56399600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:56390200-56401400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:56390200-56401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:56390400-56400000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:56390600-56403800	Weak transcription	Thymus	Thymus
17	chr6:56390800-56398400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:56390800-56402400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:56390800-56403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:56391000-56398800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:56391200-56398600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:56391400-56398400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:56391400-56398600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:56391400-56400000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:56391400-56400800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:56391400-56400800	Weak transcription	Esophagus	oesophagus
27	chr6:56391400-56400800	Weak transcription	Right Ventricle	heart
28	chr6:56391400-56401200	Weak transcription	Right Atrium	heart
29	chr6:56391400-56402200	Weak transcription	Lung	lung
30	chr6:56391400-56402400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:56391400-56402800	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:56391600-56399800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:56392000-56399200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:56392000-56400800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:56392200-56398400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:56392200-56401600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:56392400-56401600	Strong transcription	Adipose Nuclei	Adipose
38	chr6:56392400-56406200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:56392600-56399400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:56393000-56401400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:56393000-56402000	Weak transcription	Fetal Heart	heart
42	chr6:56393400-56398400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:56393600-56400600	Weak transcription	Fetal Brain Male	brain
44	chr6:56394600-56399600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:56394800-56400800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:56394800-56401000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:56395000-56399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:56395000-56399800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:56395000-56401400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:56395400-56400000	Strong transcription	HSMM	muscle

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