Variant report

Variant	rs6005870
Chromosome Location	chr22:29171244-29171245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
2	chr22:29168270..29171327-chr22:29194850..29198169,6	MCF-7	breast:
3	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
4	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
5	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
6	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10427858	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12330071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2206061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228260	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41281603	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56119508	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997389	0.89[AFR][1000 genomes]
rs5997390	0.89[AFR][1000 genomes]
rs5997401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005856	0.89[AFR][1000 genomes]
rs6005861	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005874	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005899	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005923	0.86[EUR][1000 genomes]
rs6005924	0.86[EUR][1000 genomes]
rs6005926	0.86[EUR][1000 genomes]
rs60116790	0.97[AFR][1000 genomes]
rs73388803	0.89[AFR][1000 genomes]
rs9306460	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9620826	0.97[AFR][1000 genomes]
rs9620828	0.97[AFR][1000 genomes]
rs9620833	0.89[AFR][1000 genomes]
rs9625547	0.80[AFR][1000 genomes]
rs9625548	0.94[AFR][1000 genomes]
rs9625551	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625554	0.86[AFR][1000 genomes]
rs9625562	0.81[AFR][1000 genomes]
rs9625565	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625568	0.97[AFR][1000 genomes]
rs9625572	0.97[AFR][1000 genomes]
rs9625575	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9625580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29172000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:29169800-29172000	Weak transcription	Gastric	stomach
3	chr22:29169800-29172000	Weak transcription	Lung	lung
4	chr22:29169800-29172000	Weak transcription	Spleen	Spleen
5	chr22:29169800-29173000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:29169800-29173600	Weak transcription	Esophagus	oesophagus
7	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
9	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
10	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr22:29170000-29171400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:29170000-29171400	Enhancers	Adipose Nuclei	Adipose
13	chr22:29170000-29171800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr22:29170000-29171800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr22:29170000-29172000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr22:29170000-29172000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr22:29170000-29172000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr22:29170000-29172000	Weak transcription	Ovary	ovary
19	chr22:29170000-29172000	Weak transcription	Right Atrium	heart
20	chr22:29170000-29172400	Strong transcription	NH-A	brain
21	chr22:29170000-29173000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:29170000-29174800	Weak transcription	K562	blood
23	chr22:29170000-29176400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr22:29170000-29176400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:29170000-29177600	Weak transcription	Aorta	Aorta
26	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
30	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr22:29170200-29171400	Weak transcription	NHLF	lung
32	chr22:29170200-29172400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:29170200-29172400	Genic enhancers	Placenta	Placenta
34	chr22:29170200-29175600	Weak transcription	NHDF-Ad	bronchial
35	chr22:29170200-29177800	Weak transcription	HMEC	breast
36	chr22:29170200-29178000	Weak transcription	Brain Anterior Caudate	brain
37	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
39	chr22:29170400-29171400	Transcr. at gene 5' and 3'	Dnd41	blood
40	chr22:29170400-29171600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr22:29170400-29171800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr22:29170400-29172000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:29170400-29172200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr22:29170400-29172200	Genic enhancers	HepG2	liver
45	chr22:29170400-29172400	Strong transcription	HSMMtube	muscle
46	chr22:29170400-29173800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr22:29170400-29173800	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr22:29170400-29173800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr22:29170400-29174000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr22:29170400-29174400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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