Variant report

Variant	rs2075752
Chromosome Location	chr19:42374836-42374837
allele	G/T
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	chr19:42374454..42377744-chr19:42431362..42433284,5	K562	blood:
2	chr19:42373799..42381047-chr19:42460989..42465067,14	K562	blood:
3	chr19:42374516..42378766-chr19:42444244..42446935,5	K562	blood:
4	chr19:42354421..42356282-chr19:42374725..42377333,2	MCF-7	breast:
5	chr19:42374823..42377954-chr19:42385843..42389445,4	MCF-7	breast:
6	chr19:42373353..42379670-chr19:42459996..42464717,12	K562	blood:
7	chr19:42374516..42376922-chr19:42442141..42445764,4	K562	blood:
8	chr19:42371951..42373649-chr19:42373763..42375308,2	MCF-7	breast:
9	chr19:42373231..42374863-chr19:42378109..42381070,2	MCF-7	breast:
10	chr19:42311919..42314019-chr19:42373613..42376038,2	K562	blood:
11	chr19:42373255..42375761-chr19:42417935..42419997,2	K562	blood:
12	chr19:42311919..42314958-chr19:42372358..42376038,3	K562	blood:
13	chr19:42374727..42377526-chr19:42531576..42534265,2	MCF-7	breast:
14	chr19:42374489..42376013-chr8:101732709..101734886,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000076928	Chromatin interaction
ENSG00000170956	Chromatin interaction
ENSG00000070756	Chromatin interaction
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10404939	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10405900	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap]
rs10414356	0.82[ASN][1000 genomes]
rs10414823	0.95[CHB][hapmap]
rs10415452	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10417985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12461099	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461131	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12976571	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12979253	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs12984383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366610	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1428922	0.85[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1457144	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1870092	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1870093	0.81[ASN][1000 genomes]
rs2008798	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2075749	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075750	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2199829	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs2290695	0.81[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2305809	0.90[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3786536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786538	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810153	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3922888	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4130852	0.82[ASN][1000 genomes]
rs4803511	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4803512	0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs58857981	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509001	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6509002	0.90[ASW][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs7248641	0.81[ASN][1000 genomes]
rs7250787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7254214	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257666	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258163	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7259596	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259967	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs734107	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs73549152	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8102670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104958	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs8106505	0.95[CHB][hapmap]
rs8113283	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs8113641	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs8113780	0.81[ASN][1000 genomes]
rs873282	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs882520	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs891167	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs899662	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap]
rs930102	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv932623	chr19:42370540-42378620	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2075752	ZNF575	cis	parietal	SCAN
rs2075752	LIG1	cis	parietal	SCAN
rs2075752	EXOC3L2	cis	cerebellum	SCAN
rs2075752	SLC1A5	cis	parietal	SCAN
rs2075752	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs2075752	GLTSCR2	cis	cerebellum	SCAN
rs2075752	PPP5C	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42365400-42375000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:42365400-42376200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:42365400-42376600	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr19:42365800-42375000	Genic enhancers	Fetal Intestine Small	intestine
5	chr19:42366000-42376000	Strong transcription	HSMMtube	muscle
6	chr19:42366400-42377600	Strong transcription	Fetal Brain Female	brain
7	chr19:42366600-42375000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:42367000-42376600	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr19:42367000-42376800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:42367200-42377200	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr19:42367400-42375600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:42367600-42375200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:42367600-42375600	Strong transcription	Right Ventricle	heart
14	chr19:42367600-42376200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:42367600-42379200	Weak transcription	Fetal Brain Male	brain
16	chr19:42367800-42375800	Strong transcription	Left Ventricle	heart
17	chr19:42367800-42376200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:42368400-42376600	Strong transcription	Brain Cingulate Gyrus	brain
19	chr19:42368600-42376200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:42368800-42376200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:42368800-42376200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:42368800-42377000	Strong transcription	Fetal Stomach	stomach
23	chr19:42368800-42377400	Strong transcription	Brain Germinal Matrix	brain
24	chr19:42369000-42376800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:42369000-42376800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr19:42369200-42376200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:42369200-42377200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:42369400-42376600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:42369400-42377600	Genic enhancers	Fetal Thymus	thymus
30	chr19:42369600-42375400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:42369600-42376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:42369600-42376400	Strong transcription	HUVEC	blood vessel
33	chr19:42369600-42376600	Strong transcription	HSMM	muscle
34	chr19:42369600-42377400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:42369600-42386400	Weak transcription	Fetal Kidney	kidney
36	chr19:42370200-42375600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:42370400-42377600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:42370600-42376200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:42370800-42375400	Genic enhancers	A549	lung
40	chr19:42370800-42376200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:42370800-42376800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:42371000-42375200	Strong transcription	Placenta	Placenta
43	chr19:42371000-42376400	Strong transcription	HMEC	breast
44	chr19:42371600-42376600	Strong transcription	Lung	lung
45	chr19:42371800-42375400	Genic enhancers	Primary T cells from cord blood	blood
46	chr19:42371800-42375400	Strong transcription	Hela-S3	cervix
47	chr19:42371800-42375600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr19:42371800-42376400	Strong transcription	Adipose Nuclei	Adipose
49	chr19:42371800-42376400	Strong transcription	Brain Substantia Nigra	brain
50	chr19:42371800-42376400	Genic enhancers	Rectal Mucosa Donor 31	rectum

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