Variant report

Variant	rs6006250
Chromosome Location	chr22:30182342-30182343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30178054..30179718-chr22:30181967..30184538,2	MCF-7	breast:
2	chr22:30181656..30186213-chr22:30190409..30196916,8	MCF-7	breast:
3	chr22:30182004..30185271-chr22:30192660..30196046,3	MCF-7	breast:
4	chr22:30174951..30177454-chr22:30180789..30183545,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1071962	0.81[ASN][1000 genomes]
rs12158466	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12159277	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12159536	0.82[EUR][1000 genomes]
rs12163073	0.82[EUR][1000 genomes]
rs12627866	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12628028	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12628234	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12628294	0.84[ASN][1000 genomes]
rs12628545	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs14115	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16987142	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988049	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17711461	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17711508	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018808	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240364	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240365	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240366	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249399	0.88[ASN][1000 genomes]
rs249402	0.88[ASN][1000 genomes]
rs28730892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57122143	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58015017	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59394320	0.90[EUR][1000 genomes]
rs5997515	0.82[EUR][1000 genomes]
rs5997518	0.90[EUR][1000 genomes]
rs5997519	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997520	1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997524	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6006234	0.82[EUR][1000 genomes]
rs6006235	0.82[EUR][1000 genomes]
rs6006238	0.82[EUR][1000 genomes]
rs6006239	0.82[EUR][1000 genomes]
rs6006241	0.90[EUR][1000 genomes]
rs6006242	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006247	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006249	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60805530	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61616383	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61736786	0.84[ASN][1000 genomes]
rs7285660	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7285800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7287777	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7289250	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7290420	0.82[EUR][1000 genomes]
rs73392899	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73394814	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73394831	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73394838	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737721	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737728	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740116	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8138165	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164600-30183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr22:30166600-30183800	Weak transcription	Aorta	Aorta
5	chr22:30166800-30182800	Weak transcription	Primary T cells from cord blood	blood
6	chr22:30166800-30183000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr22:30166800-30183400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr22:30166800-30183800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr22:30166800-30184200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr22:30167000-30183400	Weak transcription	Primary B cells from cord blood	blood
12	chr22:30167000-30183600	Weak transcription	Dnd41	blood
13	chr22:30167200-30183000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr22:30167200-30183200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr22:30167200-30183200	Weak transcription	GM12878-XiMat	blood
16	chr22:30167200-30184000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr22:30167200-30184000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr22:30167200-30187800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr22:30167400-30182800	Weak transcription	Fetal Thymus	thymus
20	chr22:30167400-30183000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr22:30167400-30183000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:30167400-30183200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr22:30167400-30183600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr22:30167400-30183800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr22:30167400-30183800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr22:30167400-30185400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr22:30167600-30183000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr22:30175400-30194000	Weak transcription	Hela-S3	cervix
29	chr22:30176800-30183600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr22:30177000-30189000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:30177200-30183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr22:30177200-30186000	Weak transcription	Fetal Kidney	kidney
33	chr22:30177400-30184400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr22:30177600-30183000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr22:30177600-30183000	Weak transcription	HUVEC	blood vessel
36	chr22:30177600-30183200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr22:30177600-30183800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr22:30178200-30184000	Weak transcription	Small Intestine	intestine
40	chr22:30178400-30183000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr22:30178400-30183400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr22:30178400-30183600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr22:30178400-30183800	Weak transcription	Brain Substantia Nigra	brain
44	chr22:30178400-30193000	Weak transcription	A549	lung
45	chr22:30178600-30183200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr22:30178600-30183400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr22:30178600-30184400	Weak transcription	Colonic Mucosa	Colon
48	chr22:30178600-30184800	Weak transcription	Colon Smooth Muscle	Colon
49	chr22:30178800-30182800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:30178800-30183000	Weak transcription	Duodenum Mucosa	Duodenum

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