Variant report

Variant	rs3799972
Chromosome Location	chr6:44823273-44823274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44816641..44819151-chr6:44821596..44823845,2	MCF-7	breast:
2	chr6:44821812..44824546-chr6:44828040..44830649,2	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1023091	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1028944	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs10456119	0.80[ASN][1000 genomes]
rs10484627	0.83[JPT][hapmap]
rs12209076	0.82[ASN][1000 genomes]
rs12525773	0.89[ASN][1000 genomes]
rs12526711	0.83[JPT][hapmap]
rs12526755	0.90[ASN][1000 genomes]
rs12527908	0.93[ASN][1000 genomes]
rs12528232	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12528762	0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs12529522	0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12530016	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12661902	0.88[ASN][1000 genomes]
rs12663530	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12663798	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13199289	0.85[ASN][1000 genomes]
rs13201942	0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs13202672	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13205113	0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13206526	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13209827	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs13211006	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs13216967	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1329715	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1360195	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1402599	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1418435	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16869119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16872574	0.94[ASN][1000 genomes]
rs17422760	0.83[JPT][hapmap]
rs1935549	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2139863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227852	1.00[CHB][hapmap]
rs227853	1.00[CHB][hapmap]
rs2894599	0.94[ASN][1000 genomes]
rs34243039	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34286542	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34577161	0.82[AMR][1000 genomes]
rs34776198	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34808716	0.80[ASN][1000 genomes]
rs34817919	0.94[ASN][1000 genomes]
rs35103634	0.90[ASN][1000 genomes]
rs35687006	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs35704584	0.90[ASN][1000 genomes]
rs35856781	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35908738	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs36105034	0.89[ASN][1000 genomes]
rs3799965	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799966	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799967	0.88[JPT][hapmap]
rs3799969	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799970	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799971	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3799973	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3799974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799976	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799977	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3799979	0.83[JPT][hapmap]
rs3799984	0.84[JPT][hapmap]
rs3799987	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs3823252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846896	0.81[ASN][1000 genomes]
rs3997503	0.82[ASN][1000 genomes]
rs4475320	0.90[ASN][1000 genomes]
rs4512220	0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4711797	0.81[AMR][1000 genomes]
rs4711803	0.80[ASN][1000 genomes]
rs4711805	0.80[ASN][1000 genomes]
rs4711809	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs4714812	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs4714825	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714827	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714828	0.83[JPT][hapmap]
rs4714829	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4714834	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs500773	0.80[ASN][1000 genomes]
rs524492	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs542444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs562016	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59945128	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs66642874	0.94[ASN][1000 genomes]
rs67597621	0.92[ASN][1000 genomes]
rs67911131	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6904015	0.89[JPT][hapmap]
rs6904584	0.93[ASN][1000 genomes]
rs6910294	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6919161	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs720988	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs720989	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72664272	0.91[ASN][1000 genomes]
rs72664273	0.93[ASN][1000 genomes]
rs72664274	0.94[ASN][1000 genomes]
rs7746032	0.82[ASN][1000 genomes]
rs7754378	0.83[JPT][hapmap]
rs7754698	0.87[JPT][hapmap]
rs7769218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296450	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9367208	0.80[ASN][1000 genomes]
rs9367211	0.82[JPT][hapmap]
rs9369514	0.83[JPT][hapmap]
rs9369516	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9395051	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9463017	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9463039	0.92[ASN][1000 genomes]
rs9463040	0.92[ASN][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs9472335	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9472376	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9472407	0.83[JPT][hapmap]
rs9472414	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs9885796	0.88[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799972	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44818000-44832200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:44818400-44823400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:44818400-44823400	Weak transcription	HSMMtube	muscle
4	chr6:44818400-44825800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:44818400-44826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:44818800-44823400	Weak transcription	Fetal Stomach	stomach
7	chr6:44818800-44823600	Weak transcription	HSMM	muscle
8	chr6:44819400-44823400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:44820000-44824600	Enhancers	Fetal Intestine Large	intestine
10	chr6:44820400-44832200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:44821600-44824800	Enhancers	Primary T cells from cord blood	blood
12	chr6:44821600-44824800	Enhancers	Fetal Intestine Small	intestine
13	chr6:44822000-44824400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:44822200-44824400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:44822400-44824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:44822600-44823400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:44822600-44823400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:44822600-44824000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:44822600-44824600	Enhancers	Fetal Heart	heart
20	chr6:44822600-44828400	Enhancers	Fetal Lung	lung
21	chr6:44822800-44823400	Enhancers	K562	blood
22	chr6:44822800-44824600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:44822800-44824600	Enhancers	Ovary	ovary
24	chr6:44822800-44824800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:44822800-44824800	Enhancers	Fetal Kidney	kidney
26	chr6:44823000-44823400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:44823000-44823800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:44823000-44824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:44823000-44826200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:44823000-44829600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:44823200-44823400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:44823200-44823600	Weak transcription	Brain Germinal Matrix	brain
33	chr6:44823200-44823600	Enhancers	Osteobl	bone
34	chr6:44823200-44823800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:44823200-44824200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr6:44823200-44824200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:44823200-44824400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr6:44823200-44824600	Enhancers	Fetal Brain Male	brain
39	chr6:44823200-44828800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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