Variant report

Variant	rs6550804
Chromosome Location	chr3:23887636-23887637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23865331..23867821-chr3:23885658..23888275,2	K562	blood:
2	chr3:23851087..23853550-chr3:23886176..23888553,3	MCF-7	breast:
3	chr3:23886226..23889396-chr3:23957247..23960174,3	MCF-7	breast:
4	chr3:23881781..23883313-chr3:23887444..23889365,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1026407	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707828	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12631785	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1471060	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1473380	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1473381	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4858092	0.86[EUR][1000 genomes]
rs4858094	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4858548	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858549	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550802	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6764154	0.80[ASN][1000 genomes]
rs6771166	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6784101	0.92[EUR][1000 genomes]
rs6789735	0.93[EUR][1000 genomes]
rs6794905	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7615009	0.82[ASN][1000 genomes]
rs7615255	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7615640	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7626431	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7648931	0.83[ASN][1000 genomes]
rs7651185	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9830778	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes]
rs9842907	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs9845287	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9869299	0.91[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 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	chr3:23853200-23893200	Weak transcription	Thymus	Thymus
2	chr3:23855000-23900200	Weak transcription	HSMM	muscle
3	chr3:23857600-23894000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:23857600-23900000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:23868000-23897800	Weak transcription	HUVEC	blood vessel
6	chr3:23868200-23893000	Weak transcription	Fetal Thymus	thymus
7	chr3:23871200-23899000	Weak transcription	Pancreas	Pancrea
8	chr3:23871400-23897400	Weak transcription	Primary T cells from cord blood	blood
9	chr3:23872000-23897400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:23873000-23887800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:23873800-23893000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:23873800-23898000	Weak transcription	NHEK	skin
13	chr3:23874400-23888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:23876800-23906800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:23878400-23887800	Weak transcription	Right Ventricle	heart
16	chr3:23878400-23898000	Weak transcription	Liver	Liver
17	chr3:23878600-23900400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:23878800-23893800	Weak transcription	Fetal Stomach	stomach
19	chr3:23878800-23900200	Weak transcription	Fetal Kidney	kidney
20	chr3:23879000-23898000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:23879000-23898200	Weak transcription	Right Atrium	heart
22	chr3:23879000-23907400	Weak transcription	K562	blood
23	chr3:23879200-23898200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:23879400-23893000	Weak transcription	Primary B cells from cord blood	blood
25	chr3:23880400-23892000	Weak transcription	Fetal Intestine Small	intestine
26	chr3:23882000-23888200	Weak transcription	HMEC	breast
27	chr3:23882200-23895000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:23882200-23897800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:23882200-23905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:23882400-23891000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:23882400-23894000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:23882400-23894000	Weak transcription	Fetal Intestine Large	intestine
33	chr3:23882400-23897800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:23882400-23898000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:23882600-23888000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:23882600-23900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:23882800-23892600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:23882800-23892800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:23882800-23898000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:23882800-23906000	Weak transcription	HepG2	liver
41	chr3:23884000-23887800	Weak transcription	Ovary	ovary
42	chr3:23884000-23889200	Weak transcription	Left Ventricle	heart
43	chr3:23884000-23897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:23884800-23897800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:23885000-23892800	Weak transcription	A549	lung
46	chr3:23885000-23898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:23885400-23898000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:23885800-23898000	Weak transcription	NHLF	lung
49	chr3:23887000-23893200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:23887000-23893400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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