Variant report

Variant	rs6003560
Chromosome Location	chr22:23558140-23558141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:23552072..23554781-chr22:23555952..23559163,4	MCF-7	breast:
2	chr22:23556699..23558232-chr22:23558323..23560690,2	MCF-7	breast:
3	chr22:23521444..23524230-chr22:23556475..23558420,3	MCF-7	breast:
4	chr22:23524791..23527515-chr22:23557976..23560778,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186716	Chromatin interaction
ENSG00000236794	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12160795	0.81[AMR][1000 genomes]
rs16997431	1.00[MEX][hapmap]
rs16998648	0.94[LWK][hapmap];0.90[AMR][1000 genomes]
rs28742008	0.90[AMR][1000 genomes]
rs5996464	1.00[MEX][hapmap]
rs5996486	0.90[AMR][1000 genomes]
rs5996487	0.90[AMR][1000 genomes]
rs5996489	0.90[AMR][1000 genomes]
rs5996491	0.90[AMR][1000 genomes]
rs5996494	0.90[AMR][1000 genomes]
rs5996495	0.90[AMR][1000 genomes]
rs5996496	0.81[AMR][1000 genomes]
rs6003552	0.90[AMR][1000 genomes]
rs6003553	0.90[AMR][1000 genomes]
rs6003554	0.81[AMR][1000 genomes]
rs6003555	0.90[AMR][1000 genomes]
rs6003557	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003559	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003561	0.90[AMR][1000 genomes]
rs6003566	0.90[AMR][1000 genomes]
rs6003567	0.90[AMR][1000 genomes]
rs6003568	0.90[AMR][1000 genomes]
rs6003569	0.90[AMR][1000 genomes]
rs7284383	0.90[AMR][1000 genomes]
rs7285367	0.90[AMR][1000 genomes]
rs7286520	0.81[AMR][1000 genomes]
rs7287313	0.91[LWK][hapmap];0.90[AMR][1000 genomes]
rs7287429	0.90[AMR][1000 genomes]
rs7288943	0.90[AMR][1000 genomes]
rs7289320	0.90[AMR][1000 genomes]
rs7290258	0.90[AMR][1000 genomes]
rs7290260	0.90[AMR][1000 genomes]
rs7290275	0.90[AMR][1000 genomes]
rs7290643	0.90[AMR][1000 genomes]
rs7291888	0.90[AMR][1000 genomes]
rs7292343	0.90[AMR][1000 genomes]
rs8136130	0.90[AMR][1000 genomes]
rs8138947	0.90[AMR][1000 genomes]
rs8141268	0.90[AMR][1000 genomes]
rs8142547	0.90[AMR][1000 genomes]
rs9608087	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915235	chr22:22971768-23650987	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
2	esv3388845	chr22:22973346-23652447	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	100 gene(s)	inside rSNPs	diseases
3	nsv531799	chr22:22993679-23642142	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
4	nsv1061433	chr22:22997799-23649107	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
5	nsv521695	chr22:22998337-23648009	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv915236	chr22:22998337-23650987	Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv588512	chr22:22998337-23667731	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv531800	chr22:23002708-23648163	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
9	nsv916593	chr22:23002709-23648790	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
10	nsv993496	chr22:23002709-23654222	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
11	nsv1067002	chr22:23007167-23643363	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv1067324	chr22:23007367-23654223	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv533839	chr22:23012013-23643223	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
14	nsv916933	chr22:23012069-23654237	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
15	nsv531801	chr22:23028586-23657804	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
16	nsv531802	chr22:23046186-23627391	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	diseases
17	nsv1060509	chr22:23055148-23648719	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
18	nsv1056324	chr22:23055148-23750989	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
19	nsv1062780	chr22:23060449-23648719	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
20	nsv948942	chr22:23063178-23645718	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
21	nsv1063200	chr22:23097177-23643224	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
22	nsv949250	chr22:23157485-23645718	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
23	nsv1057659	chr22:23400739-24138788	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
24	nsv588598	chr22:23530168-23638025	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23526400-23560800	Weak transcription	A549	lung
2	chr22:23530400-23558800	Weak transcription	Small Intestine	intestine
3	chr22:23535800-23559400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr22:23547200-23559400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr22:23547200-23560200	Weak transcription	Colonic Mucosa	Colon
6	chr22:23547400-23559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:23547600-23558800	Weak transcription	Fetal Brain Male	brain
8	chr22:23547800-23560400	Weak transcription	Fetal Intestine Large	intestine
9	chr22:23548400-23560400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr22:23552400-23564000	Enhancers	Right Ventricle	heart
11	chr22:23552600-23559800	Genic enhancers	K562	blood
12	chr22:23553200-23562600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr22:23554000-23559000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr22:23554000-23560400	Enhancers	HSMMtube	muscle
15	chr22:23554000-23570200	Enhancers	Placenta	Placenta
16	chr22:23554000-23570200	Enhancers	Left Ventricle	heart
17	chr22:23554200-23558400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr22:23554200-23564200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr22:23554400-23558800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:23554400-23560400	Enhancers	Adipose Nuclei	Adipose
21	chr22:23554800-23558600	Weak transcription	Brain Germinal Matrix	brain
22	chr22:23554800-23559000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr22:23555000-23558200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr22:23555000-23559600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:23555200-23558400	Enhancers	Primary B cells from cord blood	blood
26	chr22:23555200-23560200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr22:23555200-23560200	Weak transcription	Fetal Stomach	stomach
28	chr22:23555200-23560600	Weak transcription	Fetal Brain Female	brain
29	chr22:23555400-23558600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:23555400-23559400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr22:23555400-23560800	Weak transcription	Fetal Kidney	kidney
32	chr22:23555600-23558600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr22:23555600-23558800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:23555600-23560000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:23555600-23560600	Weak transcription	Psoas Muscle	Psoas
36	chr22:23555600-23560800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr22:23555800-23560200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr22:23556000-23558800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr22:23556200-23563600	Enhancers	Brain Substantia Nigra	brain
40	chr22:23556400-23558200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr22:23556400-23566600	Enhancers	Pancreas	Pancrea
42	chr22:23556400-23568400	Enhancers	Lung	lung
43	chr22:23556600-23558200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr22:23556600-23563200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr22:23556600-23563200	Genic enhancers	Right Atrium	heart
46	chr22:23556800-23558200	Enhancers	Fetal Thymus	thymus
47	chr22:23556800-23559400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:23556800-23560000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr22:23557000-23559400	Weak transcription	Fetal Intestine Small	intestine
50	chr22:23557000-23560200	Weak transcription	Ovary	ovary

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