Variant report

Variant	rs6461561
Chromosome Location	chr7:21474610-21474611
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21470159..21472152-chr7:21472473..21475281,2	MCF-7	breast:
2	chr7:21466062..21469694-chr7:21474540..21481280,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105866	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10269168	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10272006	0.86[ASW][hapmap];0.83[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11971316	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12668354	0.86[ASW][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12672629	0.82[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12673975	0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2158414	0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2282888	0.87[ASW][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2390539	0.82[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs28541530	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3735440	0.86[ASW][hapmap];0.83[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs40245	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41495348	0.84[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4397283	0.81[ASN][1000 genomes]
rs4722031	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6461562	0.82[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6461567	0.81[CEU][hapmap]
rs6461568	1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6948810	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6978922	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7780553	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7781732	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7798894	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7810841	0.83[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7811417	0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs9639377	0.85[CHB][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9639378	0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[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	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21468400-21490600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:21468400-21497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:21468600-21476600	Weak transcription	NHEK	skin
4	chr7:21468600-21478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:21468600-21488600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr7:21468600-21495600	Weak transcription	Fetal Intestine Large	intestine
7	chr7:21468800-21489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:21468800-21493600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:21469000-21474800	Weak transcription	A549	lung
10	chr7:21469000-21483800	Weak transcription	Adipose Nuclei	Adipose
11	chr7:21470000-21488600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:21470000-21490400	Weak transcription	Fetal Kidney	kidney
13	chr7:21470000-21497800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:21470200-21488600	Weak transcription	Gastric	stomach
15	chr7:21470200-21490600	Weak transcription	Psoas Muscle	Psoas
16	chr7:21470200-21494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:21470400-21477400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:21470400-21481000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:21470400-21488600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:21470400-21490600	Weak transcription	Pancreas	Pancrea
21	chr7:21470400-21494600	Weak transcription	Fetal Stomach	stomach
22	chr7:21470400-21516600	Weak transcription	Liver	Liver
23	chr7:21470400-21536400	Weak transcription	Esophagus	oesophagus
24	chr7:21470600-21475200	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:21470600-21477400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:21470600-21490800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr7:21471400-21480200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:21471600-21474800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr7:21471600-21488400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:21471800-21484000	Weak transcription	HUVEC	blood vessel
31	chr7:21471800-21486600	Weak transcription	Aorta	Aorta
32	chr7:21472000-21474800	Enhancers	Brain Angular Gyrus	brain
33	chr7:21472000-21483800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:21472000-21483800	Weak transcription	Fetal Lung	lung
35	chr7:21472000-21487200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:21472000-21488600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr7:21472000-21488800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:21472000-21489800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:21472000-21495200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:21472000-21495200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:21472200-21475800	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:21472200-21476000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:21472200-21478600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr7:21472200-21482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr7:21472400-21475800	Weak transcription	HepG2	liver
46	chr7:21472400-21476200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:21472400-21477000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr7:21472600-21476800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr7:21472600-21479000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:21472800-21475600	Weak transcription	Primary T cells fromperipheralblood	blood

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