Variant report

Variant	rs190203125
Chromosome Location	chr3:48958492-48958493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48956178..48958930-chr3:48964681..48967359,2	MCF-7	breast:
2	chr3:48954426..48959569-chr3:49057203..49060067,5	K562	blood:
3	chr3:48752504..48754863-chr3:48957920..48960085,2	K562	blood:
4	chr3:48831351..48833653-chr3:48957027..48958695,2	MCF-7	breast:
5	chr3:48882526..48886164-chr3:48952991..48958735,8	K562	blood:
6	chr3:48882526..48887589-chr3:48952932..48958567,11	K562	blood:
7	chr3:48956092..48958804-chr3:49057398..49059224,2	K562	blood:
8	chr3:48933374..48937590-chr3:48954193..48958596,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224424	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178537	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000178057	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv3394753	chr3:48956248-48960046	Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3340246	chr3:48956448-48960646	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	esv3461083	chr3:48956973-48960121	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	esv3346770	chr3:48957098-48959796	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
8	esv3461085	chr3:48957264-48959239	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	esv2473053	chr3:48957279-48959505	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	esv3461081	chr3:48957388-48959185	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
11	esv3461082	chr3:48957598-48959446	Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
12	esv3461087	chr3:48957674-48959474	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
13	esv3399339	chr3:48957692-48958812	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
14	esv3461084	chr3:48957723-48958853	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
15	esv3461088	chr3:48957723-48958853	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
16	esv3492991	chr3:48957754-48958781	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
17	esv3492992	chr3:48957754-48958781	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs190203125	WDR6	cis	intralobular white matter	BrainEAC
rs190203125	DAG1	cis	intralobular white matter	BrainEAC

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48957200-48965000	Weak transcription	Small Intestine	intestine
2	chr3:48957400-48959000	Weak transcription	Spleen	Spleen
3	chr3:48957400-48961400	Weak transcription	Ovary	ovary
4	chr3:48957400-49003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:48957600-48958800	Weak transcription	Pancreas	Pancrea
6	chr3:48957600-48959000	Weak transcription	Esophagus	oesophagus
7	chr3:48957600-48959000	Weak transcription	Gastric	stomach
8	chr3:48957600-48959800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:48957600-48961400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:48957600-48961400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:48957600-48964400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:48957600-48964400	Weak transcription	HSMMtube	muscle
13	chr3:48957600-48965000	Weak transcription	Fetal Kidney	kidney
14	chr3:48957600-48974400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:48957800-48958600	Enhancers	Liver	Liver
16	chr3:48957800-48958800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:48957800-48958800	Weak transcription	Primary T cells from cord blood	blood
18	chr3:48957800-48958800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:48957800-48958800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:48957800-48958800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:48957800-48958800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:48957800-48958800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:48957800-48958800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:48957800-48958800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:48957800-48958800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:48957800-48958800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:48957800-48958800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:48957800-48958800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:48957800-48958800	Weak transcription	Adipose Nuclei	Adipose
30	chr3:48957800-48958800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:48957800-48958800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:48957800-48958800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:48957800-48958800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:48957800-48958800	Weak transcription	Placenta	Placenta
35	chr3:48957800-48958800	Weak transcription	Fetal Thymus	thymus
36	chr3:48957800-48958800	Weak transcription	Psoas Muscle	Psoas
37	chr3:48957800-48958800	Weak transcription	Osteobl	bone
38	chr3:48957800-48959000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:48957800-48959000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:48957800-48959000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:48957800-48959000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48957800-48959000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:48957800-48959000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:48957800-48959000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:48957800-48959000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:48957800-48959000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:48957800-48959000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:48957800-48959000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:48957800-48959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:48957800-48959000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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