Variant report

Variant	rs4258824
Chromosome Location	chr2:191395027-191395028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:191394951-191395435	GM12878	blood:	n/a	n/a
2	ZNF143	chr2:191394950-191395367	GM12878	blood:	n/a	n/a
3	SETDB1	chr2:191394881-191395451	U2OS	brain:	n/a	n/a
4	TEAD4	chr2:191394890-191395599	K562	blood:	n/a	n/a
5	RCOR1	chr2:191394817-191395424	K562	blood:	n/a	n/a
6	MAX	chr2:191394828-191395157	K562	blood:	n/a	n/a
7	KAP1	chr2:191394781-191395577	HEK293	kidney:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:191393388..191396315-chr2:191446782..191449171,2	K562	blood:
2	chr2:191385869..191388991-chr2:191394619..191398567,3	K562	blood:
3	chr2:191393746..191397306-chr2:191397440..191402907,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233654	TF binding region
TMEM194B	TF binding region
ENSG00000189362	Chromatin interaction
ENSG00000233654	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10084203	0.81[ASN][1000 genomes]
rs10174174	0.82[ASN][1000 genomes]
rs10188341	0.84[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10190082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10197348	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10432434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1128723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11885992	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12052514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470863	0.80[ASN][1000 genomes]
rs12472081	0.90[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476782	0.84[YRI][hapmap]
rs12477369	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12693579	0.94[ASN][1000 genomes]
rs13417431	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16832765	0.90[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2192010	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35818159	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129082	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4261750	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4287794	0.87[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340549	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4371384	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4439990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4853510	0.98[ASN][1000 genomes]
rs4853710	0.89[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4853713	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4853716	0.98[ASN][1000 genomes]
rs56127319	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56342910	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58568707	0.89[EUR][1000 genomes]
rs59929070	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60915953	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61709084	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62180992	0.82[ASN][1000 genomes]
rs62181018	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181019	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181020	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181029	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62181034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62181052	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62182865	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182885	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62182897	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6712426	0.98[ASN][1000 genomes]
rs6727669	0.98[ASN][1000 genomes]
rs6731287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7567059	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569128	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7581762	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7581986	0.84[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7593240	0.81[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4258824	MFSD6	cis	cerebellum	SCAN
rs4258824	HIBCH	cis	parietal	SCAN
rs4258824	INPP1	cis	cerebellum	SCAN
rs4258824	HIBCH	cis	cerebellum	SCAN
rs4258824	INPP1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191357200-191398200	Weak transcription	Fetal Kidney	kidney
2	chr2:191362800-191398200	Weak transcription	Fetal Brain Male	brain
3	chr2:191365200-191398000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:191365800-191397400	Weak transcription	Liver	Liver
5	chr2:191375200-191398600	Weak transcription	Ovary	ovary
6	chr2:191376000-191397800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:191379400-191397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:191379400-191398200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:191382600-191398400	Weak transcription	Psoas Muscle	Psoas
10	chr2:191385400-191397200	Weak transcription	Thymus	Thymus
11	chr2:191385600-191396000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:191387400-191398600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:191390400-191395800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:191390800-191397400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:191391000-191397200	Enhancers	Primary T cells from cord blood	blood
16	chr2:191391200-191398400	Weak transcription	Small Intestine	intestine
17	chr2:191391200-191398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:191392400-191395600	Enhancers	Hela-S3	cervix
19	chr2:191392400-191396000	Enhancers	HepG2	liver
20	chr2:191392400-191397000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:191392600-191397000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:191392600-191397400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:191392800-191396200	Enhancers	Fetal Intestine Large	intestine
24	chr2:191392800-191396400	Enhancers	K562	blood
25	chr2:191393000-191395600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:191393000-191395600	Enhancers	Placenta	Placenta
27	chr2:191393000-191395800	Enhancers	Primary B cells from cord blood	blood
28	chr2:191393000-191395800	Enhancers	Stomach Mucosa	stomach
29	chr2:191393000-191396200	Enhancers	Fetal Intestine Small	intestine
30	chr2:191393000-191397800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:191393200-191395600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:191393200-191396200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:191393200-191398000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:191393200-191398200	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:191393200-191398600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:191393400-191398600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:191393400-191398600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:191393400-191398600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:191393600-191398400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:191393600-191398600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:191393800-191398400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:191394000-191395400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:191394000-191395400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:191394000-191395800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:191394000-191396200	Enhancers	Fetal Heart	heart
46	chr2:191394000-191396200	Enhancers	Left Ventricle	heart
47	chr2:191394000-191396200	Enhancers	Right Atrium	heart
48	chr2:191394000-191396400	Enhancers	Fetal Thymus	thymus
49	chr2:191394000-191398000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr2:191394000-191398200	Enhancers	Fetal Lung	lung

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