Variant report

Variant	rs6828574
Chromosome Location	chr4:7916326-7916327
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10049998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11932843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115701	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13131154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13137140	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13139805	0.81[CHB][hapmap]
rs13140004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145572	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13146302	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13147998	0.90[ASN][1000 genomes]
rs1317111	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1320069	0.81[JPT][hapmap]
rs1320070	0.81[JPT][hapmap]
rs1320073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13435273	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13435730	0.81[JPT][hapmap]
rs17770147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17770177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17770447	0.81[CHB][hapmap]
rs17833038	0.81[CHB][hapmap]
rs1814873	0.81[JPT][hapmap]
rs2067842	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2385902	0.89[CHB][hapmap]
rs28394221	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28492032	0.96[AMR][1000 genomes]
rs28539821	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28546404	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28605531	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28613311	0.87[ASN][1000 genomes]
rs28626087	0.85[AMR][1000 genomes]
rs28631977	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28644432	0.81[ASN][1000 genomes]
rs28673208	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28688265	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28754920	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2891927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34072304	0.91[ASN][1000 genomes]
rs34075381	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34092549	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34119140	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34121576	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34132874	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34181918	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34189407	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34221000	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34383852	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34392913	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34570748	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34598003	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34652148	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34712341	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34868842	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34869495	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34909423	0.91[ASN][1000 genomes]
rs34982807	0.91[ASN][1000 genomes]
rs35114566	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35138920	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35152796	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35154266	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35238070	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35349192	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35502845	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35727635	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35735994	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35881667	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35905776	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35933973	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35967175	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36013696	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36046241	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36106793	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3934540	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4234831	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4235268	0.81[JPT][hapmap]
rs4256209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4296663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4345163	0.81[JPT][hapmap]
rs4361385	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4411970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4443285	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4447865	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4487321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579115	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs4689860	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4689865	0.83[JPT][hapmap]
rs4689875	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4696742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696779	0.81[CHB][hapmap]
rs4696834	0.81[JPT][hapmap]
rs5012708	0.81[JPT][hapmap]
rs62289341	0.94[ASN][1000 genomes]
rs62289351	0.94[ASN][1000 genomes]
rs6446624	0.82[ASN][1000 genomes]
rs6446625	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6446627	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6446629	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6824266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6826598	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829505	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837845	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838055	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845014	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6848540	0.81[CHB][hapmap]
rs6855982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6856371	0.83[JPT][hapmap]
rs6856795	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs71600561	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71601887	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71601888	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71601889	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71601890	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs71601892	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7660568	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682202	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7682611	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7683285	0.86[JPT][hapmap]
rs7691386	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694106	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7697255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS 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	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
3	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
4	chr4:7911200-7917000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:7911400-7917400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:7912000-7918000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
8	chr4:7912600-7917000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:7912600-7917200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:7912800-7931200	Weak transcription	Gastric	stomach
11	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:7913200-7917400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:7913200-7918200	Weak transcription	Colonic Mucosa	Colon
16	chr4:7913200-7919400	Weak transcription	Right Atrium	heart
17	chr4:7913200-7919600	Weak transcription	Lung	lung
18	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:7913400-7917800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:7913400-7918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:7913400-7918800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:7913400-7919800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:7913600-7916400	Enhancers	A549	lung
24	chr4:7913600-7918000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
26	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:7913600-7930400	Weak transcription	NHEK	skin
28	chr4:7913800-7919600	Weak transcription	Adipose Nuclei	Adipose
29	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:7914000-7917000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:7914000-7917200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:7914000-7917200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:7914000-7917800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:7914000-7917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:7914000-7917800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:7914000-7918400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:7914000-7919200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:7914000-7919400	Weak transcription	Fetal Intestine Small	intestine
39	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:7914200-7917000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:7914200-7917000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:7914200-7917000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:7914200-7917000	Weak transcription	NH-A	brain
44	chr4:7914200-7917200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:7914200-7917400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:7914200-7918200	Weak transcription	Brain Germinal Matrix	brain
47	chr4:7914200-7918800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:7914200-7919600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:7914200-7919600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle

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