Variant report

Variant	rs4946967
Chromosome Location	chr6:109678572-109678573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109676926..109679753-chr6:109685240..109687572,2	K562	blood:
2	chr6:109668992..109672376-chr6:109675520..109680148,6	K562	blood:
3	chr6:109666918..109669416-chr6:109676939..109680789,3	MCF-7	breast:
4	chr6:109675179..109679333-chr6:109679553..109683129,6	K562	blood:
5	chr6:109676841..109678668-chr6:109702275..109704595,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10457192	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs10457194	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs10457195	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs1046943	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs1074765	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1074766	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10872033	0.91[EUR][1000 genomes]
rs11153171	0.87[CHB][hapmap]
rs11153183	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs11251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11754455	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs12194061	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs12197180	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs12198938	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs12199154	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs12212476	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs12214147	0.91[EUR][1000 genomes]
rs12529733	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs13219952	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13220915	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs1406899	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs1476387	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1521907	0.95[EUR][1000 genomes]
rs17070591	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1853330	0.86[EUR][1000 genomes]
rs1885690	0.95[EUR][1000 genomes]
rs1885691	0.95[EUR][1000 genomes]
rs2024850	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2024853	0.92[CEU][hapmap]
rs2211288	0.95[EUR][1000 genomes]
rs2236084	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs2277113	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2277114	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2884037	0.96[CEU][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs35146243	0.85[EUR][1000 genomes]
rs3734652	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs3757230	0.94[EUR][1000 genomes]
rs3757231	0.95[EUR][1000 genomes]
rs3757235	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3778474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778478	0.86[EUR][1000 genomes]
rs3799842	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs3818933	0.96[EUR][1000 genomes]
rs4636056	0.91[EUR][1000 genomes]
rs4945831	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946970	0.94[EUR][1000 genomes]
rs4946976	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58644322	0.95[EUR][1000 genomes]
rs59597139	0.87[EUR][1000 genomes]
rs6911838	0.84[CHB][hapmap]
rs6914216	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920372	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6939548	0.86[EUR][1000 genomes]
rs6939953	0.94[EUR][1000 genomes]
rs699700	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730089	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs736830	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs746794	0.94[EUR][1000 genomes]
rs7748669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7751582	0.91[EUR][1000 genomes]
rs7754650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755941	0.91[CEU][hapmap]
rs7768973	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7773950	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs8465	0.96[EUR][1000 genomes]
rs910730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9320286	0.93[EUR][1000 genomes]
rs9372213	0.84[EUR][1000 genomes]
rs9386799	0.80[EUR][1000 genomes]
rs9480947	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs9480949	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480956	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs9480958	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487064	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9487066	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9487069	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487070	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs9487076	0.96[EUR][1000 genomes]
rs9487084	0.94[EUR][1000 genomes]
rs9487085	0.92[EUR][1000 genomes]
rs9487103	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs974034	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs9791241	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4946967	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs4946967	SMPD2	cis	Whole Blood	GTEx
rs4946967	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs4946967	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109662600-109682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:109665600-109680400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:109669000-109683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:109671000-109681600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:109671200-109680200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:109671200-109681400	Weak transcription	Brain Anterior Caudate	brain
7	chr6:109672000-109683000	Weak transcription	Esophagus	oesophagus
8	chr6:109673000-109680200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:109673200-109681600	Weak transcription	Pancreas	Pancrea
10	chr6:109673600-109680400	Weak transcription	Spleen	Spleen
11	chr6:109673600-109681800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:109673600-109683000	Weak transcription	Psoas Muscle	Psoas
13	chr6:109673600-109683200	Weak transcription	HMEC	breast
14	chr6:109673600-109683400	Weak transcription	Gastric	stomach
15	chr6:109673600-109683400	Weak transcription	HUVEC	blood vessel
16	chr6:109673600-109687000	Weak transcription	Right Ventricle	heart
17	chr6:109673800-109682800	Weak transcription	Stomach Mucosa	stomach
18	chr6:109674000-109683000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:109674000-109683200	Weak transcription	Small Intestine	intestine
20	chr6:109674400-109681800	Strong transcription	Adipose Nuclei	Adipose
21	chr6:109674600-109680600	Strong transcription	Left Ventricle	heart
22	chr6:109675000-109684600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:109675000-109691800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:109675000-109692600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:109675000-109693200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr6:109675000-109694400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr6:109675000-109694600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr6:109675000-109700800	Strong transcription	Placenta	Placenta
29	chr6:109675200-109684400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:109675200-109688800	Strong transcription	Primary T cells from cord blood	blood
31	chr6:109675200-109693200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:109675400-109691400	Strong transcription	Osteobl	bone
33	chr6:109676800-109680800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:109676800-109693800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:109677000-109679000	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr6:109677000-109679000	Strong transcription	Fetal Stomach	stomach
37	chr6:109677000-109679400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr6:109677000-109683400	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr6:109677000-109684200	Strong transcription	Brain Hippocampus Middle	brain
40	chr6:109677000-109687200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:109677000-109698200	Strong transcription	Fetal Intestine Large	intestine
42	chr6:109677200-109678600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr6:109677200-109678600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:109677200-109678600	ZNF genes & repeats	HSMM	muscle
45	chr6:109677200-109678800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
46	chr6:109677200-109678800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:109677200-109678800	ZNF genes & repeats	Thymus	Thymus
48	chr6:109677200-109679000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:109677200-109679000	Strong transcription	Colonic Mucosa	Colon
50	chr6:109677200-109679000	Strong transcription	Ovary	ovary

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