Variant report

Variant	rs3802003
Chromosome Location	chr7:128169979-128169980
allele	A/C
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	HEY1	chr7:128169674-128172791	K562	blood:	n/a	chr7:128171836-128171851 chr7:128171698-128171713 chr7:128171495-128171510 chr7:128171252-128171267 chr7:128170601-128170616
2	POLR2A	chr7:128169713-128170095	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:128169768-128170726	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr7:128169696-128172876	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:128169583-128173092	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:60554358..60557025-chr7:128169837..128172731,3	MCF-7	breast:
2	chr7:128154968..128157377-chr7:128169188..128171020,2	K562	blood:
3	chr7:128116465..128119803-chr7:128169321..128173196,4	MCF-7	breast:
4	chr7:128044227..128046158-chr7:128169736..128172586,2	K562	blood:
5	chr17:60555522..60557036-chr7:128169502..128171568,2	MCF-7	breast:
6	chr7:128094511..128096087-chr7:128168839..128171295,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL2B-1	chr7:128169669-128170972	XLOC_006240

Variant related genes	Relation type
ENSG00000242588	TF binding region
ENSG00000165055	Chromatin interaction
ENSG00000135245	Chromatin interaction
ENSG00000146872	Chromatin interaction
ENSG00000106348	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000240758	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10228542	0.80[MEX][hapmap]
rs17152065	0.80[MEX][hapmap]
rs7779455	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794896	chr7:128142170-128170380	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3326672	chr7:128169741-128173589	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3802003	OPN1SW	cis	cerebellum	SCAN
rs3802003	RBM28	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128163600-128170400	Weak transcription	Lung	lung
2	chr7:128163800-128170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:128163800-128170000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:128163800-128170000	Weak transcription	Stomach Mucosa	stomach
5	chr7:128163800-128170000	Weak transcription	NH-A	brain
6	chr7:128163800-128170200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:128163800-128170200	Weak transcription	Fetal Thymus	thymus
8	chr7:128164000-128170200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:128164400-128170000	Weak transcription	Fetal Lung	lung
10	chr7:128164400-128170000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:128164400-128170000	Weak transcription	Hela-S3	cervix
12	chr7:128164400-128170200	Weak transcription	Colonic Mucosa	Colon
13	chr7:128164400-128170200	Weak transcription	Fetal Intestine Large	intestine
14	chr7:128164400-128170200	Weak transcription	Fetal Intestine Small	intestine
15	chr7:128164400-128170200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:128164400-128170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:128166200-128170000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:128166600-128170000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:128166600-128170000	Weak transcription	HMEC	breast
20	chr7:128166600-128170200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:128169200-128170000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:128169200-128170000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr7:128169200-128170200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:128169200-128173000	Active TSS	Stomach Smooth Muscle	stomach
25	chr7:128169600-128170000	Enhancers	Brain Hippocampus Middle	brain
26	chr7:128169600-128170200	Enhancers	Primary B cells from peripheral blood	blood
27	chr7:128169600-128170200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr7:128169600-128170200	Enhancers	Fetal Muscle Leg	muscle
29	chr7:128169600-128170200	Enhancers	Placenta	Placenta
30	chr7:128169600-128174200	Active TSS	Fetal Brain Female	brain
31	chr7:128169800-128170000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:128169800-128170000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:128169800-128170000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:128169800-128170000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr7:128169800-128170000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:128169800-128170000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:128169800-128170000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:128169800-128170000	Active TSS	Primary hematopoietic stem cells	blood
39	chr7:128169800-128170000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr7:128169800-128170000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr7:128169800-128170000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:128169800-128170000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr7:128169800-128170000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:128169800-128170000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:128169800-128170000	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr7:128169800-128170000	Enhancers	Brain Germinal Matrix	brain
47	chr7:128169800-128170000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:128169800-128170000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr7:128169800-128170000	Flanking Active TSS	Psoas Muscle	Psoas
50	chr7:128169800-128170000	Enhancers	Rectal Mucosa Donor 29	rectum

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