Variant report

Variant	rs28735417
Chromosome Location	chr1:78317565-78317566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1166698	0.85[CHB][hapmap];0.82[TSI][hapmap]
rs278853	1.00[GIH][hapmap]
rs6424659	0.92[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs6699769	0.83[ASW][hapmap];0.85[CHB][hapmap]
rs6702939	0.92[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap]
rs7525870	0.95[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap]
rs9726525	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv947433	chr1:78310844-78325736	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28735417	DNAJB4	cis	parietal	SCAN
rs28735417	NEXN	cis	multi-tissue	Pritchard
rs28735417	NEXN	cis	lymphoblastoid	seeQTL
rs28735417	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs28735417	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78280600-78325600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:78284600-78333000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:78285600-78332000	Weak transcription	Spleen	Spleen
5	chr1:78286400-78333200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:78286600-78328400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:78290200-78334200	Weak transcription	Gastric	stomach
8	chr1:78295200-78318400	Weak transcription	Ovary	ovary
9	chr1:78296800-78329000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:78298400-78340400	Weak transcription	Colonic Mucosa	Colon
11	chr1:78298600-78327000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:78298600-78352400	Weak transcription	Right Ventricle	heart
13	chr1:78298800-78332800	Weak transcription	Fetal Kidney	kidney
14	chr1:78299400-78340200	Weak transcription	NHEK	skin
15	chr1:78299400-78341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:78299600-78340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:78299600-78343000	Weak transcription	K562	blood
18	chr1:78299600-78353800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:78300200-78331600	Weak transcription	Lung	lung
20	chr1:78300200-78332600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:78300800-78320600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:78300800-78328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:78300800-78342200	Weak transcription	Fetal Brain Male	brain
24	chr1:78301400-78325600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:78301400-78332800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:78301400-78353200	Weak transcription	HSMMtube	muscle
27	chr1:78301800-78342400	Weak transcription	NHLF	lung
28	chr1:78302000-78332000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:78302800-78334200	Weak transcription	HepG2	liver
30	chr1:78303800-78326000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:78303800-78332800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:78304000-78320600	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:78305800-78319000	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:78305800-78319200	Weak transcription	Brain Anterior Caudate	brain
35	chr1:78305800-78320800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:78305800-78332200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:78305800-78342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:78306000-78342600	Weak transcription	Brain Angular Gyrus	brain
39	chr1:78309200-78328800	Weak transcription	NH-A	brain
40	chr1:78309200-78352400	Weak transcription	Aorta	Aorta
41	chr1:78309400-78320000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:78309400-78324400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:78309400-78324600	Weak transcription	Liver	Liver
44	chr1:78309400-78325600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:78309400-78326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:78309600-78330200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:78309800-78317600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:78309800-78319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:78309800-78319800	Weak transcription	Brain Germinal Matrix	brain
50	chr1:78309800-78320600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links