Variant report

Variant	rs10401746
Chromosome Location	chr19:39320960-39320961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:
2	chr19:39225035..39229236-chr19:39320225..39324035,5	K562	blood:
3	chr19:39224613..39228237-chr19:39319464..39324480,6	MCF-7	breast:
4	chr19:39220357..39220927-chr19:39320917..39321769,2	MCF-7	breast:
5	chr19:39137520..39139996-chr19:39320132..39324117,5	MCF-7	breast:
6	chr19:39302343..39304498-chr19:39319820..39321966,2	MCF-7	breast:
7	chr19:39292786..39294819-chr19:39320796..39322447,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171747	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000182472	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10405685	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap];1.00[ASN][1000 genomes]
rs13346505	1.00[ASN][1000 genomes]
rs2017784	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs73537640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537642	1.00[ASN][1000 genomes]
rs8100689	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100781	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112471	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39304400-39321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:39305200-39321600	Strong transcription	Fetal Stomach	stomach
3	chr19:39305400-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:39305600-39321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:39307400-39321800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:39310400-39321600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:39311800-39321200	Weak transcription	Stomach Mucosa	stomach
8	chr19:39311800-39321400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:39313800-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:39314000-39321400	Weak transcription	Esophagus	oesophagus
11	chr19:39315200-39321200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:39315600-39321000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:39316000-39321400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:39316000-39321600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:39316200-39321400	Genic enhancers	Placenta	Placenta
16	chr19:39316600-39321200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:39316600-39321400	Strong transcription	Fetal Lung	lung
18	chr19:39316600-39321600	Weak transcription	HUVEC	blood vessel
19	chr19:39317200-39321000	Strong transcription	Thymus	Thymus
20	chr19:39317600-39321000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:39317800-39321000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:39317800-39321200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:39317800-39321400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:39317800-39321400	Genic enhancers	Fetal Intestine Large	intestine
25	chr19:39318000-39321200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:39318000-39321200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:39318200-39321000	Strong transcription	Fetal Kidney	kidney
28	chr19:39318200-39321200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:39318400-39321000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:39318400-39321000	Weak transcription	Pancreas	Pancrea
31	chr19:39318400-39321200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:39318400-39321400	Strong transcription	Fetal Muscle Leg	muscle
33	chr19:39318400-39321600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:39318400-39321600	Weak transcription	Right Atrium	heart
35	chr19:39318400-39321800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:39318600-39321000	Weak transcription	Spleen	Spleen
37	chr19:39318600-39321400	Weak transcription	Colonic Mucosa	Colon
38	chr19:39318600-39321600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:39318600-39321600	Weak transcription	Aorta	Aorta
40	chr19:39318600-39321600	Weak transcription	Ovary	ovary
41	chr19:39318600-39321600	Weak transcription	Small Intestine	intestine
42	chr19:39318800-39321400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:39319000-39321000	Weak transcription	Primary B cells from cord blood	blood
44	chr19:39319000-39321000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:39319000-39321000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr19:39319000-39321200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr19:39319000-39321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:39319000-39321400	Weak transcription	Brain Angular Gyrus	brain
49	chr19:39319000-39321600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:39319000-39321600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links