Variant report

Variant	rs7254100
Chromosome Location	chr19:39173486-39173487
allele	A/C
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39150654..39152913-chr19:39172186..39173857,2	MCF-7	breast:
2	chr19:39173346..39178089-chr19:39336778..39344017,10	MCF-7	breast:
3	chr19:39169983..39173495-chr19:39173704..39177059,4	K562	blood:
4	chr19:39157020..39159393-chr19:39170595..39173839,3	MCF-7	breast:
5	chr19:39142774..39144585-chr19:39172676..39174844,2	MCF-7	breast:
6	chr19:39165775..39169288-chr19:39170285..39176842,12	K562	blood:
7	chr19:39173386..39176370-chr19:39183881..39186257,2	MCF-7	breast:
8	chr19:39161055..39163275-chr19:39172924..39175598,3	K562	blood:
9	chr19:39166293..39168892-chr19:39172787..39174443,3	MCF-7	breast:
10	chr19:39170783..39173793-chr19:39174469..39178078,4	MCF-7	breast:
11	chr19:39170809..39173774-chr19:39199187..39201318,2	K562	blood:
12	chr19:39173031..39174983-chr19:39187946..39191555,3	MCF-7	breast:
13	chr19:39127720..39130630-chr19:39171842..39174626,3	MCF-7	breast:
14	chr14:64854950..64855784-chr19:39173080..39173580,2	Hela-S3	cervix:
15	chr19:39173021..39174655-chr19:39220588..39222676,2	MCF-7	breast:
16	chr19:39172995..39175158-chr19:39322358..39324383,2	MCF-7	breast:
17	chr19:39173130..39177008-chr19:39180898..39185286,5	K562	blood:
18	chr19:39137008..39140489-chr19:39173171..39177881,5	K562	blood:
19	chr19:39122468..39125007-chr19:39173104..39174996,2	MCF-7	breast:
20	chr19:39169995..39171948-chr19:39172735..39174419,2	MCF-7	breast:
21	chr19:39147229..39149429-chr19:39172961..39174850,2	K562	blood:
22	chr19:39140411..39144509-chr19:39172304..39176724,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000267375	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10403540	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10406778	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10415219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10415646	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10421560	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083475	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12460849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12462270	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13343794	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13344413	0.91[CEU][hapmap]
rs16972767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279144	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs28488032	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28624276	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745859	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786837	0.90[EUR][1000 genomes]
rs3786839	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3786848	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810341	0.85[ASN][1000 genomes]
rs55876653	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55945853	0.81[EUR][1000 genomes]
rs56113315	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56365761	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62120083	0.81[EUR][1000 genomes]
rs62121814	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62121816	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62121818	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7252589	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107416	0.91[CEU][hapmap]
rs8111746	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs883394	0.93[EUR][1000 genomes]
rs883433	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs979971	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]
rs979972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
2	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
3	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
4	chr19:39164600-39173800	Genic enhancers	HepG2	liver
5	chr19:39164600-39178200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:39164800-39173800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:39164800-39177600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr19:39164800-39179200	Enhancers	Pancreas	Pancrea
9	chr19:39164800-39179800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:39165000-39174200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr19:39165400-39178200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:39165600-39174000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:39166000-39178200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:39166200-39173800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:39166200-39173800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:39166400-39173800	Genic enhancers	HMEC	breast
18	chr19:39167200-39173600	Enhancers	Stomach Mucosa	stomach
19	chr19:39167200-39173800	Genic enhancers	Fetal Intestine Large	intestine
20	chr19:39167200-39175600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr19:39167400-39173600	Genic enhancers	Lung	lung
22	chr19:39167400-39173800	Genic enhancers	NHLF	lung
23	chr19:39167400-39174400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:39167400-39180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:39167600-39173800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:39167600-39174000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:39167800-39174000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:39167800-39174000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr19:39167800-39175200	Weak transcription	Primary T cells from cord blood	blood
30	chr19:39168400-39177400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:39168800-39173800	Enhancers	Right Ventricle	heart
32	chr19:39169000-39174000	Genic enhancers	HSMM	muscle
33	chr19:39169200-39174000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:39169200-39174200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:39169200-39181000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr19:39169400-39173600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr19:39169400-39173600	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr19:39169400-39174000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:39169800-39173800	Genic enhancers	K562	blood
40	chr19:39170000-39177400	Enhancers	Liver	Liver
41	chr19:39170000-39183400	Enhancers	Placenta	Placenta
42	chr19:39170200-39173600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:39170200-39173800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39170200-39174200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39170200-39176800	Weak transcription	Thymus	Thymus
46	chr19:39170200-39177600	Enhancers	Primary hematopoietic stem cells	blood
47	chr19:39170200-39180000	Enhancers	Adipose Nuclei	Adipose
48	chr19:39170800-39173600	Weak transcription	Brain Angular Gyrus	brain
49	chr19:39170800-39173800	Weak transcription	Ovary	ovary
50	chr19:39170800-39174000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links