Variant report

Variant	rs2273249
Chromosome Location	chr22:31836486-31836487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31835142-31837027	GM12891	blood:	n/a	n/a
2	POLR2A	chr22:31835533-31837345	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr22:31835621-31836870	GM12892	blood:	n/a	n/a
4	POLR2A	chr22:31834731-31836606	HepG2	liver:	n/a	n/a
5	POLR2A	chr22:31836214-31836774	GM12892	blood:	n/a	n/a
6	POLR2A	chr22:31836263-31836503	GM12891	blood:	n/a	n/a
7	POLR2A	chr22:31835468-31836877	GM12878	blood:	n/a	n/a
8	POLR2A	chr22:31836247-31836497	U87	brain:	n/a	n/a
9	POLR2A	chr22:31836296-31836960	K562	blood:	n/a	n/a
10	POLR2A	chr22:31834979-31841892	K562	blood:	n/a	n/a
11	POLR2A	chr22:31835506-31836538	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr22:31836273-31837043	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr22:31836463-31836990	HL-60	blood:	n/a	n/a
14	POLR2A	chr22:31835544-31836911	K562	blood:	n/a	n/a
15	POLR2A	chr22:31835688-31837015	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr22:31835416-31836978	GM12878	blood:	n/a	n/a
17	POLR2A	chr22:31836324-31836872	K562	blood:	n/a	n/a
18	POLR2A	chr22:31835545-31836884	GM12891	blood:	n/a	n/a
19	POLR2A	chr22:31835485-31836856	HepG2	liver:	n/a	n/a
20	POLR2A	chr22:31836411-31837023	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:31829733-31836635..22:32764253-32784733	K562	blood:
2	22:31829733-31836635..22:32338420-32342898	K562	blood:
3	22:31829733-31836635..22:31978142-31983723	GM12878	blood:
4	22:31829733-31836635..22:32162110-32166713	GM12878	blood:
5	chr22:31836012..31838119-chr22:31842804..31844542,2	MCF-7	breast:
6	22:31829733-31836635..22:32012966-32043914	GM12878	blood:
7	chr22:31834066..31836776-chr22:31838775..31841114,2	K562	blood:

No data

Variant related genes	Relation type
EIF4ENIF1	TF binding region
ENSG00000232218	Chromatin interaction
ENSG00000243519	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000241954	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1001599	0.83[EUR][1000 genomes]
rs13057504	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16989439	0.89[YRI][hapmap]
rs16989527	0.89[YRI][hapmap]
rs16989611	1.00[YRI][hapmap]
rs16989642	1.00[YRI][hapmap]
rs16989647	1.00[YRI][hapmap]
rs16989655	1.00[YRI][hapmap]
rs16989698	0.88[YRI][hapmap]
rs1858821	0.95[CEU][hapmap]
rs2040533	0.95[CEU][hapmap]
rs2073857	0.95[CEU][hapmap]
rs2078803	0.95[CEU][hapmap]
rs2106294	0.95[CEU][hapmap]
rs2228619	0.95[CEU][hapmap]
rs2273251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283879	0.95[CEU][hapmap]
rs2899164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34538851	0.80[AMR][1000 genomes]
rs34545960	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4141404	0.95[CEU][hapmap]
rs4603880	0.95[CEU][hapmap]
rs4820043	0.95[CEU][hapmap]
rs4820963	0.95[CEU][hapmap]
rs5749265	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5749267	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5749268	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749270	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749283	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5749286	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs5749291	0.80[AMR][1000 genomes]
rs5749298	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5753521	0.95[CEU][hapmap]
rs5753543	0.95[CEU][hapmap]
rs5753597	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753609	0.95[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs5753610	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753612	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753613	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753615	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753618	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5753621	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753623	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs5753628	0.82[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753631	0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753632	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs5753638	0.83[CHB][hapmap]
rs5753639	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs5753648	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5753659	0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5753661	0.80[AMR][1000 genomes]
rs5753664	0.80[AMR][1000 genomes]
rs5753665	0.80[AMR][1000 genomes]
rs5753669	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs5753671	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs5753698	0.80[CEU][hapmap]
rs5994394	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997969	0.80[ASN][1000 genomes]
rs5998058	0.80[CEU][hapmap]
rs714909	0.95[CEU][hapmap]
rs715510	0.95[CEU][hapmap]
rs7284622	0.82[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7285619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7293171	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs737684	0.95[CEU][hapmap]
rs737887	0.95[CEU][hapmap]
rs738657	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs8138525	0.80[CEU][hapmap]
rs8138596	0.82[EUR][1000 genomes]
rs8139625	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8141150	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8142121	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9606830	0.95[CEU][hapmap]
rs9606839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9606843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9606846	0.80[AMR][1000 genomes]
rs9606847	0.80[AMR][1000 genomes]
rs9606848	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs9609264	0.95[CEU][hapmap]
rs9609268	0.81[EUR][1000 genomes]
rs9609276	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9609277	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9609286	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9609295	0.86[AMR][1000 genomes]
rs9609296	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9609297	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9609299	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9609303	0.80[AMR][1000 genomes]
rs9609304	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs9609329	0.82[CEU][hapmap]

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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2273249	SFI1	cis	Thyroid	GTEx
rs2273249	DRG1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31836600	Strong transcription	Placenta	Placenta
2	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:31797200-31845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr22:31797200-31846200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr22:31797200-31846400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
8	chr22:31797400-31846800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr22:31797800-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:31797800-31846800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr22:31799000-31845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr22:31799200-31846600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr22:31803600-31844600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr22:31804600-31847000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr22:31805000-31844800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr22:31805600-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:31806800-31842400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr22:31812000-31842000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr22:31813600-31845000	Strong transcription	Fetal Thymus	thymus
20	chr22:31814000-31838000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:31814000-31841200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr22:31814000-31846400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr22:31814200-31846800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr22:31814400-31845600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr22:31814400-31845800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr22:31814400-31846800	Strong transcription	Fetal Intestine Large	intestine
27	chr22:31814600-31841400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:31814600-31841600	Strong transcription	Lung	lung
29	chr22:31814800-31844600	Strong transcription	Thymus	Thymus
30	chr22:31814800-31846600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr22:31815000-31841400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr22:31815000-31844600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr22:31815000-31846600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr22:31815000-31846800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr22:31815000-31868200	Strong transcription	Dnd41	blood
36	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:31815400-31844400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr22:31815400-31844400	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr22:31815400-31846200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr22:31815400-31846600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr22:31815400-31846600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr22:31815600-31839200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr22:31815600-31844200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr22:31815800-31841600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr22:31816000-31839000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr22:31816200-31842200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr22:31821000-31844600	Strong transcription	Primary B cells from cord blood	blood
48	chr22:31821000-31845000	Strong transcription	Primary T cells from cord blood	blood
49	chr22:31821200-31844600	Strong transcription	Fetal Brain Female	brain
50	chr22:31822200-31846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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