Variant report

Variant	rs12460849
Chromosome Location	chr19:39143884-39143885
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39141347..39144030-chr19:39208371..39211834,3	MCF-7	breast:
2	chr19:39108181..39110451-chr19:39143165..39144685,2	MCF-7	breast:
3	chr19:39142774..39144585-chr19:39172676..39174844,2	MCF-7	breast:
4	chr19:39143284..39145449-chr19:39147356..39150112,2	K562	blood:
5	chr19:39142246..39144499-chr19:39217661..39220429,2	K562	blood:
6	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
7	chr19:39136970..39140096-chr19:39140173..39145438,10	MCF-7	breast:
8	chr19:39140411..39144509-chr19:39172304..39176724,4	K562	blood:
9	chr19:39137026..39140722-chr19:39142479..39146305,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10403540	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10404257	0.90[ASN][1000 genomes]
rs10406778	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10415219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415646	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10421560	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11083475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12462270	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs13343794	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13344413	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs16972767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28488032	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28624276	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745859	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3786839	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3786848	0.81[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3810341	0.95[ASN][1000 genomes]
rs55876653	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56113315	0.81[EUR][1000 genomes]
rs56365761	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121814	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121816	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62121818	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs7252589	0.84[ASN][1000 genomes]
rs7254100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8107416	0.92[CEU][hapmap]
rs8111746	0.80[ASN][1000 genomes]
rs883433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs979971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs979972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39138600-39152200	Transcr. at gene 5' and 3'	A549	lung
2	chr19:39140400-39146800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr19:39140800-39145200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:39141000-39144000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:39141200-39144400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:39141200-39144400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr19:39141200-39145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:39141200-39147000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr19:39141200-39147600	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:39141200-39148600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:39141200-39148800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
14	chr19:39141400-39144400	Enhancers	Primary B cells from cord blood	blood
15	chr19:39141400-39145400	Enhancers	Fetal Kidney	kidney
16	chr19:39141400-39146000	Enhancers	Brain Anterior Caudate	brain
17	chr19:39141400-39146400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr19:39141400-39147000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:39141400-39147800	Enhancers	Small Intestine	intestine
20	chr19:39141400-39148000	Genic enhancers	Fetal Muscle Leg	muscle
21	chr19:39141600-39144200	Flanking Active TSS	NHEK	skin
22	chr19:39141600-39145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:39141800-39144400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:39141800-39144600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:39141800-39146800	Enhancers	Fetal Lung	lung
26	chr19:39141800-39147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:39142000-39144000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr19:39142000-39144000	Enhancers	Left Ventricle	heart
29	chr19:39142000-39144200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39142000-39144800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr19:39142000-39147000	Enhancers	Brain Angular Gyrus	brain
32	chr19:39142000-39149400	Enhancers	Liver	Liver
33	chr19:39142200-39144000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:39142200-39144400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:39142200-39144600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:39142200-39144600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:39142200-39145400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr19:39142200-39145600	Weak transcription	Fetal Brain Female	brain
39	chr19:39142200-39146800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr19:39142200-39151800	Enhancers	Brain Cingulate Gyrus	brain
41	chr19:39142400-39149400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr19:39142600-39150400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39142800-39144000	Flanking Active TSS	K562	blood
44	chr19:39142800-39145000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr19:39142800-39151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:39143000-39144000	Enhancers	Esophagus	oesophagus
47	chr19:39143000-39146400	Enhancers	Fetal Brain Male	brain
48	chr19:39143000-39149800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr19:39143200-39144000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr19:39143200-39144200	Weak transcription	Brain Germinal Matrix	brain

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