Variant report

Variant	rs10136352
Chromosome Location	chr14:35334555-35334556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr14:35334516-35334746	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:35331154..35334713-chr14:35340036..35344743,5	K562	blood:
2	chr14:35332142..35334655-chr14:35339932..35342885,2	MCF-7	breast:

Variant related genes	Relation type
BAZ1A	TF binding region
ENSG00000258738	Chromatin interaction
ENSG00000198604	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10150083	0.88[JPT][hapmap]
rs1200414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12323749	0.87[ASN][1000 genomes]
rs12323750	0.87[ASN][1000 genomes]
rs12431818	0.81[JPT][hapmap]
rs12433706	0.90[JPT][hapmap]
rs12435778	0.81[JPT][hapmap]
rs12436798	0.91[ASN][1000 genomes]
rs12587021	0.80[JPT][hapmap]
rs12590112	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12879437	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379337	0.81[CHD][hapmap]
rs1400745	0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs17102726	0.81[JPT][hapmap]
rs17102768	0.81[JPT][hapmap]
rs17102795	0.84[JPT][hapmap]
rs17102829	0.90[JPT][hapmap]
rs1741196	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17526787	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2383677	0.90[JPT][hapmap]
rs28472856	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34072166	0.81[JPT][hapmap]
rs35153498	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783314	0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783315	0.81[JPT][hapmap]
rs3783316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7140479	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7140651	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7140903	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7148400	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7153289	0.90[JPT][hapmap]
rs72678789	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799673	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs799677	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799678	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs799679	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799680	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799681	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799682	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs799683	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8005470	0.81[JPT][hapmap]
rs8005659	0.81[CHD][hapmap]
rs8007965	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8010579	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv85205	chr14:35329756-35335693	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv976829	chr14:35332947-35341310	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10136352	SNX6	cis	parietal	SCAN
rs10136352	BRMS1L	cis	cerebellum	SCAN
rs10136352	PSMA6	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35269400-35341600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr14:35276200-35342400	Weak transcription	Pancreas	Pancrea
3	chr14:35312200-35336200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:35312600-35335200	Weak transcription	Right Ventricle	heart
5	chr14:35312800-35336600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr14:35312800-35341400	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:35312800-35341600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:35312800-35341600	Weak transcription	Psoas Muscle	Psoas
9	chr14:35312800-35342200	Weak transcription	Small Intestine	intestine
10	chr14:35312800-35342400	Weak transcription	Left Ventricle	heart
11	chr14:35313600-35341600	Weak transcription	Brain Germinal Matrix	brain
12	chr14:35318400-35342200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr14:35321800-35342400	Weak transcription	Gastric	stomach
14	chr14:35322600-35341400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr14:35322800-35341200	Weak transcription	HSMMtube	muscle
16	chr14:35322800-35342200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr14:35323200-35341800	Weak transcription	NHLF	lung
18	chr14:35323800-35342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr14:35324600-35335200	Weak transcription	Lung	lung
20	chr14:35324600-35341600	Weak transcription	Fetal Lung	lung
21	chr14:35324600-35342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr14:35324800-35342200	Weak transcription	Ovary	ovary
23	chr14:35327000-35341600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr14:35327000-35342400	Weak transcription	Esophagus	oesophagus
25	chr14:35327200-35342400	Weak transcription	Spleen	Spleen
26	chr14:35327400-35338600	Weak transcription	K562	blood
27	chr14:35327600-35335200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr14:35327600-35336400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr14:35327600-35336600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:35327600-35337200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr14:35327600-35341200	Weak transcription	Thymus	Thymus
32	chr14:35327600-35341400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr14:35327800-35341600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr14:35328200-35334800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr14:35328400-35336600	Weak transcription	NHEK	skin
36	chr14:35328400-35337400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr14:35329600-35336600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr14:35329600-35337600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:35329600-35338200	Weak transcription	Fetal Thymus	thymus
40	chr14:35329600-35342200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr14:35330000-35341400	Weak transcription	Fetal Intestine Large	intestine
42	chr14:35330000-35341600	Weak transcription	Fetal Intestine Small	intestine
43	chr14:35330000-35341600	Weak transcription	Fetal Stomach	stomach
44	chr14:35330200-35337200	Weak transcription	Fetal Muscle Leg	muscle
45	chr14:35331200-35335200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr14:35331200-35336400	Weak transcription	Primary T cells from cord blood	blood
47	chr14:35331200-35340400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr14:35331200-35341200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr14:35331200-35341400	Weak transcription	NHDF-Ad	bronchial
50	chr14:35331200-35341600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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