Variant report

Variant	rs9676315
Chromosome Location	chr19:40856325-40856326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:
2	chr19:40855052..40856726-chr19:40865449..40867831,2	MCF-7	breast:
3	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
4	chr19:40855517..40857078-chr19:40875905..40878728,2	K562	blood:
5	chr19:40853787..40856715-chr19:40882110..40885015,2	K562	blood:
6	chr19:40854917..40856679-chr19:40945662..40948462,2	MCF-7	breast:
7	chr19:40853920..40856703-chr19:40862603..40866302,4	K562	blood:

Variant related genes	Relation type
ENSG00000105223	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000206925	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10412156	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs10422945	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13345497	1.00[TSI][hapmap]
rs13346024	1.00[TSI][hapmap]
rs268665	1.00[MEX][hapmap]
rs28529139	1.00[TSI][hapmap]
rs4150995	1.00[TSI][hapmap]
rs55860305	0.96[AFR][1000 genomes];1.00[AMR][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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9676315	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40855400-40857400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:40855400-40859200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:40855400-40864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr19:40855600-40856400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr19:40855600-40856400	Enhancers	Brain Hippocampus Middle	brain
6	chr19:40855600-40856400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr19:40855600-40856600	Enhancers	Psoas Muscle	Psoas
8	chr19:40855600-40856800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr19:40855600-40857200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:40855600-40857400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:40855600-40857400	Weak transcription	Brain Angular Gyrus	brain
12	chr19:40855600-40857600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:40855600-40857800	Weak transcription	Fetal Stomach	stomach
14	chr19:40855600-40859200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr19:40855600-40859800	Weak transcription	Fetal Intestine Small	intestine
16	chr19:40855600-40861400	Weak transcription	Stomach Mucosa	stomach
17	chr19:40855600-40861600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:40855600-40861600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr19:40855600-40861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:40855600-40861600	Weak transcription	GM12878-XiMat	blood
21	chr19:40855600-40861800	Weak transcription	Primary T cells from cord blood	blood
22	chr19:40855600-40861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr19:40855600-40861800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:40855600-40861800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:40855600-40861800	Weak transcription	Brain Germinal Matrix	brain
26	chr19:40855600-40861800	Weak transcription	Ovary	ovary
27	chr19:40855600-40861800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:40855600-40861800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr19:40855600-40862200	Weak transcription	Adipose Nuclei	Adipose
30	chr19:40855600-40862600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:40855600-40862800	Weak transcription	Brain Anterior Caudate	brain
32	chr19:40855600-40862800	Weak transcription	Fetal Lung	lung
33	chr19:40855600-40863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:40855600-40863200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:40855600-40863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:40855600-40863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr19:40855600-40863600	Weak transcription	Fetal Brain Female	brain
38	chr19:40855600-40863800	Weak transcription	Liver	Liver
39	chr19:40855600-40864000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:40855600-40864000	Weak transcription	Spleen	Spleen
41	chr19:40855600-40864000	Weak transcription	NH-A	brain
42	chr19:40855600-40864400	Weak transcription	Placenta	Placenta
43	chr19:40855600-40865200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:40855600-40865200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:40855600-40865200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:40855600-40865200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:40855600-40865200	Weak transcription	Thymus	Thymus
48	chr19:40855600-40865200	Weak transcription	A549	lung
49	chr19:40855600-40865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:40855600-40865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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