Variant report

Variant	rs3799973
Chromosome Location	chr6:44823727-44823728
allele	A/G
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: 222 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:222)

rs_ID	r²[population]
rs1023090	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs1023091	0.84[CHB][hapmap]
rs1028944	0.83[CHB][hapmap]
rs1041332	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1041333	0.83[ASN][1000 genomes]
rs10456119	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10484627	0.81[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10948176	0.91[YRI][hapmap]
rs10948183	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs10948185	0.81[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10948186	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs10948187	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10948188	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10948190	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10948192	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs10948193	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10948194	0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948197	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10948198	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1150806	0.87[ASN][1000 genomes]
rs11524119	0.80[ASN][1000 genomes]
rs1159131	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs11967188	0.94[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12190136	0.87[ASN][1000 genomes]
rs12190513	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12191518	0.90[ASN][1000 genomes]
rs12192367	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs12196818	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12197442	0.82[ASN][1000 genomes]
rs12198904	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12200412	0.83[ASN][1000 genomes]
rs12205071	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs12207620	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12209076	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12214778	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12215263	0.92[YRI][hapmap]
rs12524069	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12525009	0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12526711	0.88[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs12527908	0.82[ASN][1000 genomes]
rs12528232	0.83[CHB][hapmap]
rs12528762	0.84[CHB][hapmap]
rs12529490	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs12529522	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12530016	0.81[JPT][hapmap]
rs1293457	0.87[ASN][1000 genomes]
rs1293467	0.87[ASN][1000 genomes]
rs1293598	0.91[ASN][1000 genomes]
rs1293600	0.86[ASN][1000 genomes]
rs13196587	0.86[ASN][1000 genomes]
rs13199289	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13201942	0.83[CHB][hapmap]
rs13202672	0.85[ASN][1000 genomes]
rs13203495	0.84[ASN][1000 genomes]
rs13205113	0.84[CHB][hapmap]
rs13206526	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs13209827	0.84[CHB][hapmap]
rs13211229	0.86[ASN][1000 genomes]
rs13213412	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13215618	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs13216116	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1329710	0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1329713	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1329714	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs1329715	0.83[CHB][hapmap]
rs1329716	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1342370	0.83[ASN][1000 genomes]
rs1360195	0.83[CHB][hapmap]
rs1360197	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1402599	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1418434	0.83[ASN][1000 genomes]
rs1521355	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1557143	0.87[ASN][1000 genomes]
rs1576382	0.83[ASN][1000 genomes]
rs1578676	0.90[ASN][1000 genomes]
rs1590864	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16869119	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs16872574	0.82[ASN][1000 genomes]
rs17339124	0.86[ASN][1000 genomes]
rs17422760	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17424547	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1831310	0.83[ASN][1000 genomes]
rs1854547	0.85[ASN][1000 genomes]
rs1891411	0.87[ASN][1000 genomes]
rs1891412	0.87[ASN][1000 genomes]
rs1935549	0.83[ASN][1000 genomes]
rs1935551	0.86[ASN][1000 genomes]
rs1971482	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs1980265	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2038555	0.81[ASN][1000 genomes]
rs2038556	0.83[ASN][1000 genomes]
rs2038557	0.83[ASN][1000 genomes]
rs2040032	0.83[ASN][1000 genomes]
rs2139863	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs227849	0.94[CHB][hapmap]
rs2396369	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2396370	0.85[ASN][1000 genomes]
rs2396371	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2396372	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs2894599	0.82[ASN][1000 genomes]
rs34243039	0.87[ASN][1000 genomes]
rs34776198	0.84[ASN][1000 genomes]
rs34808716	0.93[ASN][1000 genomes]
rs34817919	0.82[ASN][1000 genomes]
rs34982599	0.85[ASN][1000 genomes]
rs35357222	0.86[ASN][1000 genomes]
rs35687006	0.83[CHB][hapmap]
rs35813980	0.86[ASN][1000 genomes]
rs35856781	0.87[ASN][1000 genomes]
rs3778507	0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs3799965	0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799966	0.83[ASN][1000 genomes]
rs3799967	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3799968	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799969	0.84[ASN][1000 genomes]
rs3799970	0.84[ASN][1000 genomes]
rs3799971	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3799972	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3799974	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs3799976	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799977	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3799979	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3799981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs3799984	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3799986	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs3799987	0.83[CHB][hapmap]
rs3823252	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3846896	0.94[ASN][1000 genomes]
rs3957281	0.92[ASN][1000 genomes]
rs4398713	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs4412189	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4512220	0.84[CHB][hapmap]
rs4711798	0.83[ASN][1000 genomes]
rs4711799	0.87[ASN][1000 genomes]
rs4711803	0.94[ASN][1000 genomes]
rs4711805	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4711807	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4711809	0.94[CHB][hapmap]
rs4714819	0.82[ASN][1000 genomes]
rs4714820	0.81[ASN][1000 genomes]
rs4714821	0.86[ASN][1000 genomes]
rs4714822	0.83[ASN][1000 genomes]
rs4714825	0.83[ASN][1000 genomes]
rs4714827	0.87[ASN][1000 genomes]
rs4714828	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4714830	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4714832	0.83[ASN][1000 genomes]
rs4714834	0.83[CHB][hapmap]
rs4714836	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs472672	0.91[ASN][1000 genomes]
rs472673	0.85[ASN][1000 genomes]
rs494982	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs500773	0.94[ASN][1000 genomes]
rs524492	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs538801	0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs542444	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs55893720	0.86[ASN][1000 genomes]
rs562016	0.83[ASN][1000 genomes]
rs567054	0.84[ASN][1000 genomes]
rs588848	0.91[ASN][1000 genomes]
rs608941	0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs62438007	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62438011	0.80[ASN][1000 genomes]
rs636845	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6458414	0.90[ASN][1000 genomes]
rs6458415	0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs66642874	0.82[ASN][1000 genomes]
rs67597621	0.81[ASN][1000 genomes]
rs67911131	0.80[ASN][1000 genomes]
rs679713	0.90[ASN][1000 genomes]
rs6903576	0.90[ASN][1000 genomes]
rs6904015	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6904584	0.82[ASN][1000 genomes]
rs6910294	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6910749	0.87[ASN][1000 genomes]
rs6919161	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs6919485	0.84[ASN][1000 genomes]
rs6923519	0.91[ASN][1000 genomes]
rs6924185	0.83[YRI][hapmap]
rs6925017	0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs6925467	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs718112	0.93[ASN][1000 genomes]
rs720988	0.84[ASN][1000 genomes]
rs720989	0.82[ASN][1000 genomes]
rs72664272	0.80[ASN][1000 genomes]
rs72664273	0.82[ASN][1000 genomes]
rs72664274	0.82[ASN][1000 genomes]
rs7742360	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7747642	0.91[ASN][1000 genomes]
rs7749865	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7754378	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7754698	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7763421	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs7769218	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7775717	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs929614	0.87[ASN][1000 genomes]
rs9357459	0.87[ASN][1000 genomes]
rs9357464	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9367208	0.94[ASN][1000 genomes]
rs9367210	0.91[YRI][hapmap]
rs9367211	0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9369512	0.87[ASN][1000 genomes]
rs9369513	0.86[ASN][1000 genomes]
rs9369514	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9369516	0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9369529	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs9395049	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9395051	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9395055	0.90[ASN][1000 genomes]
rs9463039	0.81[ASN][1000 genomes]
rs9463040	0.81[ASN][1000 genomes]
rs9463054	0.84[ASN][1000 genomes]
rs9463055	0.84[ASN][1000 genomes]
rs9472360	0.83[ASN][1000 genomes]
rs9472376	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9472383	0.90[ASN][1000 genomes]
rs9472407	0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs9472409	0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9472411	0.86[ASN][1000 genomes]
rs9472416	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs969211	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs976699	0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3799973	SUPT3H	cis	multi-tissue	Pritchard
rs3799973	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 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	chr6:44818400-44825800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:44818400-44826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:44820000-44824600	Enhancers	Fetal Intestine Large	intestine
5	chr6:44820400-44832200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:44821600-44824800	Enhancers	Primary T cells from cord blood	blood
7	chr6:44821600-44824800	Enhancers	Fetal Intestine Small	intestine
8	chr6:44822000-44824400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:44822200-44824400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:44822400-44824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:44822600-44824000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:44822600-44824600	Enhancers	Fetal Heart	heart
13	chr6:44822600-44828400	Enhancers	Fetal Lung	lung
14	chr6:44822800-44824600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:44822800-44824600	Enhancers	Ovary	ovary
16	chr6:44822800-44824800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:44822800-44824800	Enhancers	Fetal Kidney	kidney
18	chr6:44823000-44823800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:44823000-44824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:44823000-44826200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:44823000-44829600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:44823200-44823800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:44823200-44824200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:44823200-44824200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:44823200-44824400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:44823200-44824600	Enhancers	Fetal Brain Male	brain
27	chr6:44823200-44828800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:44823400-44823800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:44823400-44824200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:44823400-44824400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:44823400-44824400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:44823400-44824400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:44823400-44824600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:44823400-44824600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:44823400-44824600	Enhancers	Fetal Stomach	stomach
36	chr6:44823400-44824600	Enhancers	NHDF-Ad	bronchial
37	chr6:44823400-44824800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:44823400-44826600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:44823600-44824000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:44823600-44824200	Flanking Active TSS	Osteobl	bone
41	chr6:44823600-44824400	Enhancers	Adipose Nuclei	Adipose
42	chr6:44823600-44824400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:44823600-44824600	Enhancers	Colon Smooth Muscle	Colon
44	chr6:44823600-44824600	Enhancers	HSMM	muscle
45	chr6:44823600-44827200	Enhancers	Brain Germinal Matrix	brain
46	chr6:44823600-44828000	Weak transcription	HSMMtube	muscle

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