Variant report

Variant	rs6005875
Chromosome Location	chr22:29174423-29174424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29172058..29177577-chr22:29178390..29181662,9	MCF-7	breast:
2	chr22:29174303..29175888-chr22:29187835..29189460,2	MCF-7	breast:
3	chr22:29165791..29171536-chr22:29171828..29178249,15	MCF-7	breast:
4	chr22:29167384..29172904-chr22:29173066..29177227,7	K562	blood:

Variant related genes	Relation type
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12159764	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1547424	0.80[ASN][1000 genomes]
rs16986714	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894590	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269575	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41281601	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484131	0.83[ASN][1000 genomes]
rs4645087	0.80[ASN][1000 genomes]
rs57652775	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59954406	0.87[ASN][1000 genomes]
rs5997399	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997400	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997403	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997404	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005876	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005879	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005893	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005900	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005905	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005906	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005907	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005918	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005920	0.87[ASN][1000 genomes]
rs60513698	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6519764	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7284322	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290958	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291783	0.83[ASN][1000 genomes]
rs73388819	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388827	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73388828	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73388838	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73388841	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73399615	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73399621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9941965	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	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
4	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	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
3	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
4	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29170000-29174800	Weak transcription	K562	blood
6	chr22:29170000-29176400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr22:29170000-29176400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:29170000-29177600	Weak transcription	Aorta	Aorta
9	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
13	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr22:29170200-29175600	Weak transcription	NHDF-Ad	bronchial
15	chr22:29170200-29177800	Weak transcription	HMEC	breast
16	chr22:29170200-29178000	Weak transcription	Brain Anterior Caudate	brain
17	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
19	chr22:29170400-29175400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:29170400-29175600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr22:29170400-29177800	Strong transcription	Fetal Intestine Large	intestine
22	chr22:29170400-29183800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr22:29170400-29184000	Strong transcription	Fetal Muscle Leg	muscle
24	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:29170600-29174600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr22:29170600-29184600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr22:29170600-29184800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr22:29170800-29174600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr22:29170800-29174600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr22:29170800-29175000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr22:29170800-29175000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr22:29170800-29175000	Weak transcription	Psoas Muscle	Psoas
36	chr22:29170800-29179800	Weak transcription	Fetal Brain Male	brain
37	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr22:29171000-29174800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr22:29171000-29175400	Weak transcription	Colon Smooth Muscle	Colon
40	chr22:29171000-29175600	Strong transcription	Fetal Intestine Small	intestine
41	chr22:29171000-29175800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr22:29171000-29176400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr22:29171000-29176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr22:29171000-29178000	Weak transcription	Brain Angular Gyrus	brain
45	chr22:29171000-29179600	Weak transcription	Small Intestine	intestine
46	chr22:29171000-29185600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr22:29171200-29174600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr22:29171200-29174800	Strong transcription	Fetal Lung	lung
49	chr22:29171200-29176400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr22:29171200-29177000	Weak transcription	Brain Hippocampus Middle	brain

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