Variant report

Variant	rs5997404
Chromosome Location	chr22:29189446-29189447
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29186661..29189525-chr22:29705422..29708097,2	MCF-7	breast:
2	chr22:29162995..29164989-chr22:29188685..29191039,2	MCF-7	breast:
3	chr22:29188183..29190691-chr22:29223821..29225664,2	K562	blood:
4	chr22:28986053..28988845-chr22:29188910..29191071,2	K562	blood:
5	chr22:29137327..29140027-chr22:29189364..29191172,3	MCF-7	breast:
6	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:
7	chr22:29134319..29139472-chr22:29186598..29194420,8	K562	blood:
8	chr22:29174303..29175888-chr22:29187835..29189460,2	MCF-7	breast:
9	chr22:29189258..29191243-chr22:29893230..29895527,2	K562	blood:
10	chr22:29002103..29004832-chr22:29188346..29190789,2	MCF-7	breast:
11	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
12	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
13	chr22:28995890..28998730-chr22:29188380..29190809,3	MCF-7	breast:
14	chr22:29154766..29156419-chr22:29187780..29189689,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185340	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12159764	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs132530	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs1547424	0.81[ASN][1000 genomes]
rs16986714	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269575	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41281601	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4484131	0.84[ASN][1000 genomes]
rs4645087	0.81[ASN][1000 genomes]
rs57652775	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59954406	0.88[ASN][1000 genomes]
rs5997399	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005875	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005876	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005878	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005900	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005906	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005915	0.83[ASW][hapmap];0.84[YRI][hapmap]
rs6005918	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005920	0.88[ASN][1000 genomes]
rs60513698	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6519764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7284322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7290019	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290679	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290958	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7291783	0.83[ASN][1000 genomes]
rs73388819	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388827	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73388828	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73388838	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73388841	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73399615	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73399621	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9941965	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
3	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
5	chr22:29176800-29190200	Weak transcription	Hela-S3	cervix
6	chr22:29180400-29191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:29180600-29191000	Weak transcription	Small Intestine	intestine
8	chr22:29180800-29189800	Weak transcription	HMEC	breast
9	chr22:29180800-29190200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:29181600-29191000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr22:29182000-29191000	Weak transcription	Fetal Brain Male	brain
12	chr22:29182400-29190000	Weak transcription	Stomach Mucosa	stomach
13	chr22:29182400-29190000	Weak transcription	HSMMtube	muscle
14	chr22:29182400-29190000	Weak transcription	NHEK	skin
15	chr22:29182400-29190200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr22:29182400-29190800	Weak transcription	Gastric	stomach
17	chr22:29182400-29191200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:29182600-29189800	Weak transcription	NHLF	lung
19	chr22:29182600-29190200	Weak transcription	A549	lung
20	chr22:29182600-29190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr22:29182600-29191000	Weak transcription	Ovary	ovary
22	chr22:29182600-29191200	Weak transcription	Esophagus	oesophagus
23	chr22:29182800-29190000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr22:29182800-29190000	Weak transcription	Right Ventricle	heart
25	chr22:29182800-29190400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:29183000-29190000	Weak transcription	Brain Anterior Caudate	brain
27	chr22:29183000-29190000	Weak transcription	Fetal Kidney	kidney
28	chr22:29183000-29190000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr22:29183000-29190200	Weak transcription	K562	blood
30	chr22:29183200-29189800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:29183200-29190000	Weak transcription	Brain Substantia Nigra	brain
32	chr22:29183400-29190000	Weak transcription	Psoas Muscle	Psoas
33	chr22:29183600-29190000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr22:29183600-29190200	Genic enhancers	Dnd41	blood
35	chr22:29183600-29191000	Weak transcription	Spleen	Spleen
36	chr22:29183800-29190000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr22:29183800-29190200	Weak transcription	Colonic Mucosa	Colon
38	chr22:29183800-29191000	Weak transcription	Aorta	Aorta
39	chr22:29184000-29190000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr22:29184200-29190600	Weak transcription	Brain Germinal Matrix	brain
41	chr22:29184400-29189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr22:29184400-29190000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr22:29184400-29190000	Weak transcription	Brain Angular Gyrus	brain
44	chr22:29184400-29190000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr22:29184400-29190000	Weak transcription	HUVEC	blood vessel
46	chr22:29184600-29189800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr22:29184600-29190000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr22:29185000-29189800	Weak transcription	Brain Hippocampus Middle	brain
49	chr22:29185000-29189800	Weak transcription	Colon Smooth Muscle	Colon
50	chr22:29185200-29189800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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