Variant report

Variant	rs3793859
Chromosome Location	chr10:61861872-61861873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:61861420..61862225-chr10:61968357..61968917,2	MCF-7	breast:
2	chr10:61861551..61863282-chr10:61890286..61892542,2	K562	blood:
3	chr10:61861017..61862098-chr10:61968150..61968757,3	MCF-7	breast:
4	chr10:61861377..61863286-chr10:61900763..61902506,2	MCF-7	breast:
5	chr10:61860379..61863071-chr10:61864008..61865521,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151150	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10218875	0.88[JPT][hapmap]
rs10740007	0.85[ASN][1000 genomes]
rs10740008	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10740009	0.88[JPT][hapmap]
rs10761452	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10761453	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761454	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10821671	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10821674	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10821675	0.83[ASN][1000 genomes]
rs10994194	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10994195	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10994200	0.90[ASN][1000 genomes]
rs10994210	0.88[JPT][hapmap]
rs11596260	0.84[CEU][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs12146176	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12779035	1.00[ASW][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2241540	0.84[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2393585	0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2393600	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34577721	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3750800	0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs3793858	0.96[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7077937	0.82[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3793859	RTKN2	cis	parietal	SCAN
rs3793859	SLC16A9	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61792200-61883200	Weak transcription	Psoas Muscle	Psoas
2	chr10:61834000-61868000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:61835400-61870000	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:61835400-61883200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:61835600-61874600	Weak transcription	Brain Anterior Caudate	brain
6	chr10:61835600-61883000	Weak transcription	Fetal Heart	heart
7	chr10:61835800-61866400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:61836000-61865200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:61836000-61874800	Weak transcription	HSMMtube	muscle
10	chr10:61836000-61881800	Weak transcription	Left Ventricle	heart
11	chr10:61836000-61893200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:61836200-61864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:61836200-61870000	Weak transcription	Fetal Brain Female	brain
14	chr10:61836200-61870200	Weak transcription	Fetal Stomach	stomach
15	chr10:61838800-61864000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:61839800-61876400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:61841200-61899400	Weak transcription	Right Ventricle	heart
18	chr10:61843000-61864800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:61843000-61868600	Weak transcription	Ovary	ovary
20	chr10:61846600-61864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr10:61846600-61864600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr10:61846600-61888600	Weak transcription	Fetal Kidney	kidney
23	chr10:61847000-61863000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr10:61847000-61868200	Weak transcription	Primary T cells from cord blood	blood
25	chr10:61847200-61865600	Weak transcription	Aorta	Aorta
26	chr10:61848000-61863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:61848000-61874200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr10:61848000-61900400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:61848200-61863200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:61848200-61868000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:61848200-61868200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:61848200-61874800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr10:61848400-61889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr10:61849200-61865000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:61849200-61882600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:61851800-61869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:61855600-61863200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr10:61856400-61862200	Enhancers	Liver	Liver
39	chr10:61857200-61864000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr10:61857200-61882600	Weak transcription	NH-A	brain
41	chr10:61857400-61863400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:61857400-61865200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:61857400-61867200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr10:61857400-61889800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr10:61857600-61864000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:61857800-61864200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:61857800-61889600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:61859400-61864200	Weak transcription	Fetal Intestine Large	intestine
49	chr10:61859800-61867800	Weak transcription	Fetal Intestine Small	intestine
50	chr10:61859800-61889800	Weak transcription	Duodenum Mucosa	Duodenum

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