Variant report

Variant	rs13203252
Chromosome Location	chr6:109672736-109672737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109668456..109674736-chr6:109696300..109702886,9	K562	blood:
2	chr6:109669515..109674044-chr6:109702916..109706265,4	K562	blood:
3	chr6:109660514..109663248-chr6:109671174..109674117,2	K562	blood:
4	chr6:109665458..109673633-chr6:109699710..109704931,12	MCF-7	breast:
5	chr6:109669396..109675577-chr6:109699158..109705270,9	K562	blood:
6	chr6:109669590..109673452-chr6:109701898..109703889,4	MCF-7	breast:
7	chr6:109667528..109670285-chr6:109670801..109673728,2	K562	blood:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048203	0.84[CEU][hapmap]
rs10782162	0.89[CEU][hapmap]
rs11153174	0.84[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11153175	0.84[CEU][hapmap]
rs11753645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11757877	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11967108	0.84[CEU][hapmap];0.84[YRI][hapmap]
rs12190920	0.83[CEU][hapmap]
rs12197114	0.84[CEU][hapmap]
rs12524502	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12524639	0.84[CEU][hapmap]
rs12528566	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528712	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528822	0.84[CEU][hapmap]
rs13192476	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13195517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13199519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13220304	0.88[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs1322818	0.86[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1358998	0.84[CEU][hapmap]
rs1923725	0.84[CEU][hapmap]
rs2236582	0.84[CEU][hapmap]
rs2275650	0.84[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2275652	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34131679	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34292461	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34320275	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35452836	0.84[EUR][1000 genomes]
rs35969918	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757234	0.84[CEU][hapmap]
rs3757238	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799840	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818934	0.80[AFR][1000 genomes]
rs4428538	0.83[EUR][1000 genomes]
rs61076041	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61233650	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61318425	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67857472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929208	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7773095	0.84[CEU][hapmap]
rs9480948	0.84[CEU][hapmap]
rs9480957	0.84[CEU][hapmap]
rs9487100	0.84[CEU][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13203252	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs13203252	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13203252	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13203252	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13203252	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
5	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
6	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:109662600-109682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:109662800-109677000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:109664200-109672800	Weak transcription	HSMM	muscle
10	chr6:109665600-109677000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:109665600-109680400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:109666000-109678000	Weak transcription	Fetal Kidney	kidney
13	chr6:109666400-109675200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:109668000-109673800	Enhancers	Stomach Mucosa	stomach
15	chr6:109668000-109674000	Enhancers	Fetal Intestine Large	intestine
16	chr6:109668000-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:109668600-109674800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:109669000-109674000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:109669000-109683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:109669400-109673800	Enhancers	Colonic Mucosa	Colon
21	chr6:109669600-109677000	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:109669600-109677200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:109669800-109677200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:109670200-109673000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:109670400-109673200	Enhancers	Primary hematopoietic stem cells	blood
26	chr6:109670400-109674000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:109670600-109673200	Enhancers	Pancreas	Pancrea
28	chr6:109670800-109674400	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr6:109671000-109672800	Enhancers	Lung	lung
30	chr6:109671000-109673600	Enhancers	Gastric	stomach
31	chr6:109671000-109677800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:109671000-109681600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:109671200-109677000	Weak transcription	Aorta	Aorta
34	chr6:109671200-109677200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:109671200-109680200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:109671200-109681400	Weak transcription	Brain Anterior Caudate	brain
37	chr6:109671400-109672800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:109671400-109672800	Enhancers	Duodenum Mucosa	Duodenum
39	chr6:109671400-109672800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:109671400-109673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:109671400-109674400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:109671400-109675000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:109671400-109675000	Weak transcription	Liver	Liver
44	chr6:109671400-109675000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:109671400-109675200	Weak transcription	Ovary	ovary
46	chr6:109671400-109675400	Weak transcription	Osteobl	bone
47	chr6:109671400-109675600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:109671400-109677200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:109671400-109677200	Weak transcription	A549	lung
50	chr6:109671400-109677600	Weak transcription	HepG2	liver

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