Variant report

Variant	rs12509628
Chromosome Location	chr4:7790149-7790150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:64223802..64226025-chr4:7789518..7791033,2	MCF-7	breast:
2	chr4:7785064..7787531-chr4:7788291..7790828,3	K562	blood:
3	chr15:91412162..91414947-chr4:7788716..7790216,2	MCF-7	breast:
4	chr4:7784424..7786891-chr4:7788959..7792253,4	K562	blood:
5	chr4:7723319..7725071-chr4:7788895..7790676,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10516188	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10937859	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12501415	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12505487	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511332	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12511919	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512093	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512166	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841110	0.90[AMR][1000 genomes]
rs16841121	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16841150	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16841183	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841209	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16841268	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841283	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16841288	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269877	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285763	0.89[AMR][1000 genomes]
rs2285768	0.87[AMR][1000 genomes]
rs34002186	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56177309	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6824231	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs730420	0.92[AMR][1000 genomes]
rs73797315	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs877707	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9683902	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9790400	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9790478	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	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
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
2	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
3	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
4	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:7780200-7794400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:7780800-7790600	Weak transcription	Pancreas	Pancrea
11	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:7781200-7796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
15	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
16	chr4:7781600-7791400	Strong transcription	Fetal Intestine Large	intestine
17	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
18	chr4:7782000-7790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:7782200-7791000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr4:7782600-7790800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:7783400-7794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:7783400-7798800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:7783400-7799200	Weak transcription	HepG2	liver
24	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:7784000-7791000	Weak transcription	Spleen	Spleen
26	chr4:7784000-7792800	Weak transcription	Primary T cells from cord blood	blood
27	chr4:7784000-7794200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:7784000-7794400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
31	chr4:7784200-7790600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:7784200-7797800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:7784200-7800600	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:7784200-7800600	Weak transcription	Esophagus	oesophagus
35	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
36	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr4:7784400-7791800	Strong transcription	Fetal Stomach	stomach
38	chr4:7784400-7794000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:7784600-7791400	Strong transcription	A549	lung
40	chr4:7784800-7791400	Strong transcription	NHLF	lung
41	chr4:7784800-7792800	Strong transcription	NH-A	brain
42	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:7785000-7790600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:7785200-7791200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:7785200-7791600	Strong transcription	Fetal Muscle Leg	muscle
46	chr4:7785200-7791800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:7785200-7791800	Strong transcription	Fetal Intestine Small	intestine
48	chr4:7785200-7796200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:7785400-7790200	Strong transcription	Brain Germinal Matrix	brain
50	chr4:7785400-7791600	Strong transcription	Gastric	stomach

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