Variant report

Variant	rs165821
Chromosome Location	chr22:29877625-29877626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr22:29875358-29878062	SK-N-SH	brain:	n/a	chr22:29877653-29877662
2	EP300	chr22:29877606-29878096	H1-hESC	embryonic stem cell:	n/a	n/a
3	NANOG	chr22:29877574-29877905	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr22:29876718-29877888	K562	blood:	n/a	n/a
5	POLR2A	chr22:29875929-29877897	K562	blood:	n/a	n/a
6	E2F6	chr22:29875674-29878117	H1-hESC	embryonic stem cell:	n/a	chr22:29877137-29877146 chr22:29876212-29876224
7	CTBP2	chr22:29877603-29878003	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr22:29877588-29878045	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF143	chr22:29876341-29877960	H1-hESC	embryonic stem cell:	n/a	chr22:29877209-29877219
10	NRF1	chr22:29876483-29877798	SK-N-SH	brain:	n/a	chr22:29877136-29877147 chr22:29877136-29877150
11	MYC	chr22:29876181-29877973	K562	blood:	n/a	chr22:29877654-29877663
12	MXI1	chr22:29877546-29877913	H1-hESC	embryonic stem cell:	n/a	chr22:29877653-29877662
13	RAD21	chr22:29877554-29878029	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr22:29876079-29877944	K562	blood:	n/a	chr22:29876117-29876127 chr22:29877654-29877663
15	BACH1	chr22:29876282-29878043	H1-hESC	embryonic stem cell:	n/a	n/a
16	NR2F2	chr22:29877539-29878035	MCF-7	breast:	n/a	n/a
17	E2F6	chr22:29875801-29877672	H1-hESC	embryonic stem cell:	n/a	chr22:29877137-29877146 chr22:29876212-29876224
18	SP1	chr22:29877535-29878070	H1-hESC	embryonic stem cell:	n/a	chr22:29877808-29877820 chr22:29877808-29877819 chr22:29877809-29877819 chr22:29877809-29877823 chr22:29877809-29877818 chr22:29877810-29877819 chr22:29877808-29877820
19	YY1	chr22:29877466-29877947	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr22:29877620-29877998	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr22:29876592-29877977	K562	blood:	n/a	chr22:29877654-29877663
22	TCF12	chr22:29877597-29878055	H1-hESC	embryonic stem cell:	n/a	chr22:29877783-29877793
23	CHD2	chr22:29876574-29877980	H1-hESC	embryonic stem cell:	n/a	chr22:29877153-29877163
24	EP300	chr22:29877620-29877954	H1-hESC	embryonic stem cell:	n/a	n/a
25	TCF7L2	chr22:29877553-29877998	HCT-116	colon:	n/a	chr22:29877748-29877762 chr22:29877751-29877760
26	MYC	chr22:29877521-29877825	H1-hESC	embryonic stem cell:	n/a	chr22:29877654-29877663
27	MAX	chr22:29877539-29877693	K562	blood:	n/a	chr22:29877654-29877663
28	EP300	chr22:29877573-29878133	MCF-7	breast:	n/a	n/a
29	SP1	chr22:29877582-29878051	H1-hESC	embryonic stem cell:	n/a	chr22:29877808-29877820 chr22:29877808-29877819 chr22:29877809-29877819 chr22:29877809-29877823 chr22:29877809-29877818 chr22:29877810-29877819 chr22:29877808-29877820
30	MAX	chr22:29876147-29877975	H1-hESC	embryonic stem cell:	n/a	chr22:29877654-29877663
31	YY1	chr22:29877599-29877948	H1-hESC	embryonic stem cell:	n/a	n/a
32	FOXM1	chr22:29877619-29878110	MCF-7	breast:	n/a	n/a
33	MAX	chr22:29875631-29878091	H1-hESC	embryonic stem cell:	n/a	chr22:29876117-29876127 chr22:29877654-29877663
34	JUND	chr22:29877612-29877978	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29877072..29879814-chr22:29891846..29894236,2	MCF-7	breast:
2	chr22:29877350..29878233-chr22:29913108..29913740,2	MCF-7	breast:
3	chr22:29877541..29878058-chr22:29914348..29915105,2	MCF-7	breast:
4	chr22:29866168..29866984-chr22:29877594..29878224,2	K562	blood:
5	chr22:29876809..29879806-chr22:29881526..29883122,2	K562	blood:
6	chr22:29866353..29868086-chr22:29877604..29879531,2	K562	blood:
7	chr22:29781578..29782726-chr22:29877337..29878344,7	MCF-7	breast:
8	chr22:29877412..29878391-chr22:29912701..29914203,38	MCF-7	breast:
9	chr22:29877386..29878406-chr22:29912849..29914254,52	MCF-7	breast:
10	chr22:29876640..29878874-chr22:29919748..29922123,2	K562	blood:
11	chr22:29865857..29867643-chr22:29876448..29878393,2	MCF-7	breast:
12	chr22:29781864..29782673-chr22:29877575..29878342,2	MCF-7	breast:
13	chr22:29877043..29879359-chr22:29911623..29914922,6	MCF-7	breast:
14	chr22:29877422..29878326-chr22:29912754..29914005,18	MCF-7	breast:
15	chr22:29663630..29665723-chr22:29877193..29880137,2	K562	blood:

Variant related genes	Relation type
RFPL1S	TF binding region
ENSG00000100263	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs105268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs165602	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs165607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165624	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs165633	1.00[ASW][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.80[AFR][1000 genomes]
rs165649	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165734	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs165823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165853	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs165899	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs174649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174721	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs174722	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2008880	1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs2857634	1.00[JPT][hapmap]
rs424541	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447914	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457930	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs465736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467669	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs467768	1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs4823046	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs5752916	1.00[CEU][hapmap]
rs5752917	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5763238	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763247	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763315	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs5763347	1.00[JPT][hapmap]
rs5763348	1.00[JPT][hapmap]
rs6006219	1.00[JPT][hapmap]
rs737979	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs9306464	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608766	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9613908	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9613915	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613919	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	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
3	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv1062039	chr22:29854861-29889201	Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv438344	chr22:29856079-29886043	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3371117	chr22:29874452-29879050	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
12	nsv524511	chr22:29877417-29877625	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs165821	C22orf13	cis	parietal	SCAN
rs165821	TPST2	cis	cerebellum	SCAN
rs165821	RNF185	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29873800-29877800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
2	chr22:29873800-29877800	Bivalent Enhancer	Placenta	Placenta
3	chr22:29874600-29878000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
4	chr22:29874800-29877800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
5	chr22:29875000-29878000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr22:29875600-29877800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr22:29875800-29877800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr22:29875800-29878000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr22:29875800-29878000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr22:29875800-29878000	Enhancers	Pancreas	Pancrea
11	chr22:29875800-29878000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr22:29875800-29878200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:29875800-29878200	Bivalent Enhancer	Fetal Lung	lung
14	chr22:29875800-29878200	Flanking Active TSS	Ovary	ovary
15	chr22:29876000-29877800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:29876000-29877800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr22:29876000-29878000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
18	chr22:29876000-29878200	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr22:29876200-29878000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:29876400-29877800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
21	chr22:29876400-29877800	Bivalent Enhancer	HUVEC	blood vessel
22	chr22:29876600-29877800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr22:29876600-29878000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:29876600-29878200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
25	chr22:29876800-29877800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr22:29876800-29878000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr22:29877000-29877800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
28	chr22:29877000-29877800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr22:29877000-29877800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr22:29877000-29877800	Bivalent Enhancer	Fetal Thymus	thymus
31	chr22:29877000-29878000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:29877000-29878000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr22:29877200-29877800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:29877200-29877800	Bivalent Enhancer	Esophagus	oesophagus
35	chr22:29877200-29877800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr22:29877200-29878000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr22:29877200-29878400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr22:29877200-29878800	Enhancers	Spleen	Spleen
39	chr22:29877400-29877800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr22:29877400-29877800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:29877400-29877800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr22:29877400-29877800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:29877400-29877800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
44	chr22:29877400-29877800	Bivalent Enhancer	Right Ventricle	heart
45	chr22:29877400-29877800	Flanking Bivalent TSS/Enh	NH-A	brain
46	chr22:29877400-29878000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:29877400-29878000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr22:29877400-29878000	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr22:29877400-29878200	Enhancers	A549	lung
50	chr22:29877400-29878200	Flanking Active TSS	HSMM	muscle

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