Variant report

Variant	rs34466648
Chromosome Location	chr19:40433042-40433043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40432414..40434132-chr19:40502600..40505156,2	K562	blood:

Variant related genes	Relation type
ENSG00000187187	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1007628	0.91[CHB][hapmap]
rs10406738	0.91[CHB][hapmap]
rs10417013	0.80[ASN][1000 genomes]
rs10417043	0.80[ASN][1000 genomes]
rs163213	0.91[CHB][hapmap]
rs16973950	0.90[CHB][hapmap]
rs170901	0.91[CHB][hapmap]
rs173061	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs17796769	0.81[ASN][1000 genomes]
rs17796901	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs183504	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.80[ASN][1000 genomes]
rs186801	0.80[ASN][1000 genomes]
rs186815	0.83[CHB][hapmap]
rs2111543	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs2111544	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs2231737	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs234301	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs234302	0.91[CHB][hapmap]
rs234304	0.83[CHB][hapmap]
rs234309	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs234313	0.80[ASN][1000 genomes]
rs234315	0.80[ASN][1000 genomes]
rs234317	0.80[ASN][1000 genomes]
rs234318	0.83[CHB][hapmap]
rs234323	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs234324	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs234325	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs234326	0.80[ASN][1000 genomes]
rs234328	0.80[ASN][1000 genomes]
rs234341	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs234352	1.00[CHB][hapmap]
rs234353	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap]
rs234355	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap]
rs234361	0.83[CHB][hapmap]
rs234370	0.83[CHB][hapmap]
rs234374	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs2542303	0.80[ASN][1000 genomes]
rs2819956	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs28366011	0.80[ASN][1000 genomes]
rs337779	0.83[CHB][hapmap]
rs337785	0.82[CHB][hapmap]
rs337786	0.83[CHB][hapmap]
rs337799	0.83[CHB][hapmap]
rs365055	0.80[ASN][1000 genomes]
rs371500	0.83[CHB][hapmap]
rs372599	0.81[ASN][1000 genomes]
rs3760920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387202	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs3887029	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs392958	0.91[CHB][hapmap]
rs3930885	0.80[ASN][1000 genomes]
rs404754	0.80[ASN][1000 genomes]
rs416283	0.83[CHB][hapmap]
rs421533	0.83[CHB][hapmap]
rs426950	0.83[CHB][hapmap]
rs4577216	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap]
rs459091	0.83[CHB][hapmap]
rs57219798	0.81[ASN][1000 genomes]
rs59925663	0.81[ASN][1000 genomes]
rs60887294	0.80[ASN][1000 genomes]
rs61236589	0.80[ASN][1000 genomes]
rs7247527	0.83[CHB][hapmap]
rs73543974	0.81[ASN][1000 genomes]
rs73543979	0.81[ASN][1000 genomes]
rs73545909	0.80[ASN][1000 genomes]
rs73545911	0.80[ASN][1000 genomes]
rs73545934	0.80[ASN][1000 genomes]
rs73545936	0.80[ASN][1000 genomes]
rs73545938	0.80[ASN][1000 genomes]
rs73545945	0.80[ASN][1000 genomes]
rs73545950	0.80[ASN][1000 genomes]
rs73545955	0.80[ASN][1000 genomes]
rs73545975	0.80[ASN][1000 genomes]
rs73546001	0.80[ASN][1000 genomes]
rs73546002	0.80[ASN][1000 genomes]
rs73547618	0.80[ASN][1000 genomes]
rs73547620	0.80[ASN][1000 genomes]
rs73547638	0.80[ASN][1000 genomes]
rs8105066	0.83[CHB][hapmap]
rs8106032	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv2483	chr19:40340641-40435505	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv482218	chr19:40353963-40440533	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34466648	SERTAD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40414400-40433600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:40418200-40435800	Weak transcription	Brain Anterior Caudate	brain
3	chr19:40420200-40441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:40423400-40433600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:40423400-40435800	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:40426800-40433200	Weak transcription	Fetal Stomach	stomach
7	chr19:40428800-40434000	Strong transcription	Primary T cells from cord blood	blood
8	chr19:40430000-40440800	Weak transcription	Primary B cells from cord blood	blood
9	chr19:40431000-40433200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr19:40431400-40433200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:40431400-40435600	Weak transcription	Adipose Nuclei	Adipose
12	chr19:40431600-40433400	Enhancers	Placenta	Placenta
13	chr19:40432200-40434800	Active TSS	Fetal Intestine Large	intestine
14	chr19:40432600-40433600	Strong transcription	Colonic Mucosa	Colon
15	chr19:40432600-40434000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:40432800-40433200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr19:40432800-40433400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:40432800-40433600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:40432800-40433600	Genic enhancers	Stomach Mucosa	stomach
20	chr19:40432800-40433600	Weak transcription	K562	blood
21	chr19:40432800-40434200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
22	chr19:40433000-40433200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
23	chr19:40433000-40434200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:40433000-40434200	Enhancers	Gastric	stomach
25	chr19:40433000-40434200	Genic enhancers	Rectal Mucosa Donor 31	rectum

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