Variant report

Variant	rs13249731
Chromosome Location	chr8:8880818-8880819
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	chr8:8873907..8877820-chr8:8877960..8882381,6	K562	blood:
2	chr8:8873008..8875540-chr8:8879367..8882077,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104626	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1016512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503395	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249899	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679527	1.00[ASN][1000 genomes]
rs13250674	0.80[EUR][1000 genomes]
rs13250919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13258661	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13260103	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13261370	0.82[EUR][1000 genomes]
rs13263480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273871	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13274157	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276286	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13276537	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13281029	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1430931	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17155162	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2044389	0.85[EUR][1000 genomes]
rs28393746	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28405982	1.00[ASN][1000 genomes]
rs28516774	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28534948	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28812315	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2956245	1.00[ASN][1000 genomes]
rs2979269	0.95[YRI][hapmap]
rs34111588	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34334157	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34391124	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34412730	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34418902	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712023	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34752993	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34854114	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35227233	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35616716	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35808561	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3958881	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841092	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55634245	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55696609	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60519586	1.00[ASN][1000 genomes]
rs66483157	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66869483	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67139167	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67259528	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67434672	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67575865	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67958495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68043139	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6985908	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6989707	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990134	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6993811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994214	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6994551	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7008080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7012302	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71514525	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71514527	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73195799	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73197711	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73197712	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7387683	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7816149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7816450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
5	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13249731	THEX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861200-8892400	Weak transcription	Aorta	Aorta
2	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:8861600-8885600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:8861800-8881800	Weak transcription	Fetal Kidney	kidney
5	chr8:8861800-8883400	Weak transcription	Spleen	Spleen
6	chr8:8861800-8883600	Weak transcription	Small Intestine	intestine
7	chr8:8861800-8885200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:8861800-8887200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:8861800-8887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr8:8861800-8890000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr8:8861800-8891400	Weak transcription	Brain Angular Gyrus	brain
12	chr8:8861800-8891800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr8:8861800-8892000	Weak transcription	Brain Anterior Caudate	brain
14	chr8:8861800-8892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:8861800-8892200	Weak transcription	Ovary	ovary
16	chr8:8861800-8893800	Weak transcription	Fetal Brain Male	brain
17	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
19	chr8:8865400-8886000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr8:8870200-8883600	Weak transcription	Stomach Mucosa	stomach
21	chr8:8870600-8892200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr8:8871200-8900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:8871400-8892800	Weak transcription	HSMMtube	muscle
24	chr8:8871800-8887200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:8871800-8894400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr8:8872000-8881800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:8872000-8891200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:8872400-8887200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:8872600-8881000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr8:8873200-8882200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr8:8873600-8882200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr8:8873800-8881800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr8:8873800-8882000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr8:8873800-8884400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr8:8874800-8881400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr8:8875000-8891200	Weak transcription	Fetal Intestine Small	intestine
37	chr8:8875200-8883600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:8875200-8887200	Weak transcription	Brain Substantia Nigra	brain
39	chr8:8875200-8897200	Weak transcription	Gastric	stomach
40	chr8:8875400-8881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:8875400-8884400	Weak transcription	Brain Hippocampus Middle	brain
42	chr8:8875400-8890200	Weak transcription	Fetal Stomach	stomach
43	chr8:8875400-8892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr8:8875400-8894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr8:8875400-8897000	Weak transcription	Lung	lung
46	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
47	chr8:8875600-8882000	Weak transcription	Fetal Muscle Leg	muscle
48	chr8:8875600-8882600	Weak transcription	Psoas Muscle	Psoas
49	chr8:8875600-8886000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr8:8875600-8890000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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