Variant report

Variant	rs108816
Chromosome Location	chr22:22025670-22025671
allele	C/T
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	STAT5A	chr22:22025291-22025763	K562	blood:	n/a	n/a
2	POLR2A	chr22:22024852-22025689	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:21994969..21997353-chr22:22024513..22026345,2	MCF-7	breast:
2	chr22:22022905..22026953-chr22:22292276..22294623,3	K562	blood:
3	chr22:22024787..22025715-chr22:22292164..22292828,2	K562	blood:

Variant related genes	Relation type
PPIL2	TF binding region
ENSG00000224086	Chromatin interaction
ENSG00000273342	Chromatin interaction
ENSG00000128228	Chromatin interaction
ENSG00000100034	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10009	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1045681	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11089647	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11089651	0.90[EUR][1000 genomes]
rs11089685	0.81[AMR][1000 genomes]
rs11703445	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11705530	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11912412	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11914240	1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs12170039	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs16997333	1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs1811070	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1860	0.89[LWK][hapmap];0.84[TSI][hapmap]
rs2034570	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2034572	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070504	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2081431	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278118	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2840341	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3209602	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3747094	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap]
rs3747095	0.91[ASN][1000 genomes]
rs3788329	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804071	0.88[CEU][hapmap];0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs384262	0.84[CEU][hapmap]
rs433704	0.84[CEU][hapmap]
rs45502092	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4821168	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56387230	0.93[ASN][1000 genomes]
rs5998956	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62235078	0.84[EUR][1000 genomes]
rs62235097	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62235098	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62235099	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62235101	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs710172	0.89[LWK][hapmap];0.84[TSI][hapmap]
rs7285365	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7285388	0.91[ASN][1000 genomes]
rs7286619	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7291614	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73149915	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs741617	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8139619	1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs8142802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs861812	0.89[ASN][1000 genomes]
rs861813	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs861816	0.85[AFR][1000 genomes]
rs861836	0.88[EUR][1000 genomes]
rs915724	0.83[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9941935	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914458	chr22:21747678-22070489	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
2	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
3	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
4	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
5	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
6	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
7	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
8	nsv914464	chr22:21964761-22039863	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
9	nsv914465	chr22:21964761-22055280	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv914466	chr22:21964761-22057273	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
11	nsv531797	chr22:21977700-22959729	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	476 gene(s)	inside rSNPs	diseases
12	nsv914467	chr22:21982892-22055280	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	363 gene(s)	inside rSNPs	diseases
13	nsv914468	chr22:21982892-22070489	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	365 gene(s)	inside rSNPs	diseases
14	nsv1066403	chr22:22010822-22352262	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 target site	51 gene(s)	inside rSNPs	diseases
15	nsv510804	chr22:22024531-22132764	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs108816	SLC7A4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22021400-22026200	Weak transcription	Fetal Kidney	kidney
2	chr22:22021400-22026400	Weak transcription	Psoas Muscle	Psoas
3	chr22:22021400-22032000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:22021400-22035200	Weak transcription	Stomach Mucosa	stomach
5	chr22:22021400-22036600	Weak transcription	A549	lung
6	chr22:22022000-22055600	Weak transcription	Fetal Brain Male	brain
7	chr22:22022200-22030600	Strong transcription	Fetal Stomach	stomach
8	chr22:22022200-22053200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr22:22023400-22030600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr22:22023400-22030600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr22:22023400-22030600	Strong transcription	Fetal Muscle Leg	muscle
12	chr22:22023400-22030800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr22:22023400-22031000	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:22023400-22031200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr22:22023400-22032400	Strong transcription	Lung	lung
16	chr22:22023400-22034000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:22023600-22026200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr22:22023600-22026200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr22:22023600-22028400	Strong transcription	HepG2	liver
20	chr22:22023600-22029400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr22:22023600-22030000	Strong transcription	Fetal Thymus	thymus
22	chr22:22023600-22030400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr22:22023600-22030400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr22:22023600-22030400	Strong transcription	Primary B cells from cord blood	blood
25	chr22:22023600-22030400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr22:22023600-22030400	Strong transcription	Brain Cingulate Gyrus	brain
27	chr22:22023600-22030600	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr22:22023600-22030600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr22:22023600-22030600	Strong transcription	Adipose Nuclei	Adipose
30	chr22:22023600-22030600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr22:22023600-22030600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr22:22023600-22030600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr22:22023600-22030600	Strong transcription	K562	blood
34	chr22:22023600-22030800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr22:22023600-22032600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr22:22023600-22032600	Strong transcription	Thymus	Thymus
37	chr22:22023600-22032800	Strong transcription	Spleen	Spleen
38	chr22:22023800-22030400	Strong transcription	Brain Germinal Matrix	brain
39	chr22:22023800-22030600	Strong transcription	Primary T cells from cord blood	blood
40	chr22:22023800-22030600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr22:22023800-22030600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr22:22023800-22030600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr22:22023800-22030800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr22:22023800-22030800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr22:22023800-22030800	Strong transcription	Ovary	ovary
46	chr22:22024000-22027400	Genic enhancers	GM12878-XiMat	blood
47	chr22:22024000-22029400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr22:22024000-22029400	Strong transcription	HSMM	muscle
49	chr22:22024000-22029600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr22:22024000-22030200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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