Variant report

Variant	rs979971
Chromosome Location	chr19:39144244-39144245
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	chr19:39108181..39110451-chr19:39143165..39144685,2	MCF-7	breast:
2	chr19:39142774..39144585-chr19:39172676..39174844,2	MCF-7	breast:
3	chr19:39143284..39145449-chr19:39147356..39150112,2	K562	blood:
4	chr19:39142246..39144499-chr19:39217661..39220429,2	K562	blood:
5	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
6	chr19:39144043..39146811-chr19:39176683..39178531,2	MCF-7	breast:
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
ENSG00000178982	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10403540	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10404257	0.93[ASN][1000 genomes]
rs10406778	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415219	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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]
rs10426809	0.82[CHD][hapmap];0.80[JPT][hapmap]
rs11083475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12460849	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]
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];0.90[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16972767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[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];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786839	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs3786848	0.84[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs3810341	0.98[ASN][1000 genomes]
rs55876653	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56113315	0.81[EUR][1000 genomes]
rs56365761	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121814	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62121816	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62121818	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs7252589	0.86[ASN][1000 genomes]
rs7254100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8107416	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs8111746	0.83[ASN][1000 genomes]
rs883433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[ASN][1000 genomes]
rs979972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs979971	PSG3	cis	parietal	SCAN
rs979971	CAPN12	cis	Liver	GTEx
rs979971	ERCC1	cis	cerebellum	SCAN
rs979971	LGALS17A	cis	cerebellum	SCAN
rs979971	MEGF8	cis	parietal	SCAN
rs979971	TMEM145	cis	parietal	SCAN
rs979971	ZNF526	cis	cerebellum	SCAN
rs979971	RPS16	cis	parietal	SCAN

Chromatin state (count:122 , 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	chr19:39141200-39144400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:39141200-39144400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr19:39141200-39145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:39141200-39147000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr19:39141200-39147600	Enhancers	Primary hematopoietic stem cells	blood
10	chr19:39141200-39148600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:39141200-39148800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
13	chr19:39141400-39144400	Enhancers	Primary B cells from cord blood	blood
14	chr19:39141400-39145400	Enhancers	Fetal Kidney	kidney
15	chr19:39141400-39146000	Enhancers	Brain Anterior Caudate	brain
16	chr19:39141400-39146400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:39141400-39147000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:39141400-39147800	Enhancers	Small Intestine	intestine
19	chr19:39141400-39148000	Genic enhancers	Fetal Muscle Leg	muscle
20	chr19:39141600-39145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:39141800-39144400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:39141800-39144600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:39141800-39146800	Enhancers	Fetal Lung	lung
24	chr19:39141800-39147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:39142000-39144800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr19:39142000-39147000	Enhancers	Brain Angular Gyrus	brain
27	chr19:39142000-39149400	Enhancers	Liver	Liver
28	chr19:39142200-39144400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr19:39142200-39144600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:39142200-39144600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr19:39142200-39145400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr19:39142200-39145600	Weak transcription	Fetal Brain Female	brain
33	chr19:39142200-39146800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr19:39142200-39151800	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:39142400-39149400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr19:39142600-39150400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:39142800-39145000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr19:39142800-39151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:39143000-39146400	Enhancers	Fetal Brain Male	brain
40	chr19:39143000-39149800	Enhancers	H9 Cell Line	embryonic stem cell
41	chr19:39143200-39144600	Enhancers	Fetal Stomach	stomach
42	chr19:39143200-39146800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:39143400-39144400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:39143400-39144800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr19:39143400-39144800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:39143400-39144800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr19:39143400-39144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:39143400-39144800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:39143400-39145200	Enhancers	Fetal Heart	heart
50	chr19:39143400-39145200	Weak transcription	Dnd41	blood

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