Variant report

Variant	rs3775590
Chromosome Location	chr4:174243631-174243632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:174090877..174092412-chr4:174243600..174245281,2	K562	blood:
2	chr4:174243466..174246218-chr4:174302181..174305054,2	K562	blood:
3	chr4:174240982..174243911-chr4:174245243..174249082,5	MCF-7	breast:
4	chr4:174242458..174245436-chr4:174334949..174337241,2	MCF-7	breast:
5	chr11:62609021..62610572-chr4:174243392..174244912,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGB2-1	chr4:174243357-174243750	ENSG00000248774.1

No data

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10471199	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs10520255	0.83[JPT][hapmap]
rs11132982	0.87[ASN][1000 genomes]
rs11721513	1.00[CEU][hapmap]
rs11722602	0.86[EUR][1000 genomes]
rs11722807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724459	1.00[EUR][1000 genomes]
rs11726679	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11728029	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11729778	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731057	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11734517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736050	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151627	0.83[JPT][hapmap]
rs1481120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17059154	0.84[CHB][hapmap]
rs17059272	1.00[MEX][hapmap]
rs34885736	1.00[EUR][1000 genomes]
rs3733476	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775591	0.88[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4695829	0.88[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs56159092	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58185783	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58612091	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61470087	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6821844	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6822924	0.83[JPT][hapmap]
rs6828429	1.00[CEU][hapmap]
rs6842693	0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs6853427	0.88[ASN][1000 genomes]
rs72999543	0.82[ASN][1000 genomes]
rs73001512	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73003342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73003349	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73003362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73003376	1.00[ASN][1000 genomes]
rs73005346	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73005353	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73005356	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73005357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73005363	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7665469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7668435	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7672055	0.88[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7681398	0.81[AFR][1000 genomes]
rs7686909	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4610	chr4:174217026-174252627	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174206400-174249400	Weak transcription	Fetal Kidney	kidney
2	chr4:174210400-174253000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:174210400-174253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:174210600-174253000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:174210800-174252000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:174215200-174249600	Weak transcription	Left Ventricle	heart
7	chr4:174215200-174254000	Weak transcription	Psoas Muscle	Psoas
8	chr4:174217600-174253000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:174222400-174246800	Weak transcription	Fetal Lung	lung
10	chr4:174222800-174253000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:174223400-174250600	Strong transcription	Dnd41	blood
12	chr4:174223400-174251600	Strong transcription	Fetal Thymus	thymus
13	chr4:174223600-174250400	Weak transcription	Hela-S3	cervix
14	chr4:174225200-174250800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:174229000-174249200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:174229200-174251400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:174229200-174252400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:174229200-174253200	Weak transcription	Small Intestine	intestine
19	chr4:174229800-174247600	Weak transcription	NH-A	brain
20	chr4:174230800-174249200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:174231200-174254000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:174232400-174244000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr4:174233600-174249600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:174233800-174246000	Weak transcription	A549	lung
25	chr4:174235200-174244400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:174235600-174253000	Weak transcription	Fetal Brain Female	brain
27	chr4:174235600-174253200	Weak transcription	Colonic Mucosa	Colon
28	chr4:174236000-174253800	Weak transcription	Right Ventricle	heart
29	chr4:174236400-174253200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:174236600-174249400	Weak transcription	Brain Substantia Nigra	brain
31	chr4:174236600-174250600	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:174237000-174250600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:174237400-174254200	Weak transcription	Ovary	ovary
34	chr4:174237600-174246800	Weak transcription	Spleen	Spleen
35	chr4:174237600-174253200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:174237600-174254000	Weak transcription	Esophagus	oesophagus
37	chr4:174237600-174254400	Weak transcription	Pancreas	Pancrea
38	chr4:174237800-174249400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:174237800-174253200	Weak transcription	Gastric	stomach
40	chr4:174238200-174249000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:174238200-174253200	Weak transcription	Aorta	Aorta
42	chr4:174238400-174246200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:174238400-174246800	Weak transcription	Fetal Stomach	stomach
44	chr4:174238400-174253000	Weak transcription	Fetal Intestine Small	intestine
45	chr4:174238400-174254400	Weak transcription	Lung	lung
46	chr4:174239800-174244000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:174240000-174249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:174240000-174251800	Weak transcription	Brain Germinal Matrix	brain
49	chr4:174240400-174245600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:174240400-174250200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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