Variant report

Variant	rs964549
Chromosome Location	chr4:22453260-22453261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22452403..22454410-chr4:22458067..22459809,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10938897	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13102647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13109695	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13135121	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13140185	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13140367	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1462995	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1462996	1.00[JPT][hapmap]
rs1462997	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1564135	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs16872669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1841824	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs1841825	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1841828	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1947738	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4583743	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4611916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4627850	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6448155	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs71182940	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[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	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
3	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
4	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:22400800-22461800	Weak transcription	Gastric	stomach
8	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
10	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
11	chr4:22422000-22453400	Weak transcription	Esophagus	oesophagus
12	chr4:22424400-22457800	Weak transcription	Dnd41	blood
13	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
15	chr4:22429400-22457800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:22430600-22456000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:22432400-22460400	Weak transcription	Small Intestine	intestine
18	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:22434000-22461200	Weak transcription	Brain Anterior Caudate	brain
20	chr4:22434800-22456000	Weak transcription	Brain Substantia Nigra	brain
21	chr4:22436800-22456200	Weak transcription	NHEK	skin
22	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:22437800-22453400	Weak transcription	Fetal Heart	heart
24	chr4:22437800-22459600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:22439200-22458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:22443400-22472400	Weak transcription	Ovary	ovary
29	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
30	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr4:22443600-22476200	Weak transcription	A549	lung
32	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:22445800-22456600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:22447000-22455600	Weak transcription	Pancreas	Pancrea
36	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
37	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:22447200-22475000	Weak transcription	NHLF	lung
39	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
40	chr4:22448000-22461400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:22448200-22455000	Weak transcription	HepG2	liver
42	chr4:22448400-22456000	Weak transcription	Fetal Kidney	kidney
43	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
44	chr4:22449200-22453800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:22449400-22457000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:22449600-22458200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr4:22450200-22453400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:22450200-22453400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:22450200-22453600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:22450200-22455200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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