Variant report

Variant	rs1863408
Chromosome Location	chr4:187869954-187869955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:187641888..187650885-chr4:187865376..187870322,9	MCF-7	breast:
2	chr4:187644629..187648780-chr4:187865976..187870182,7	MCF-7	breast:
3	chr4:187867684..187870026-chr4:187872421..187875152,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083857	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11728508	0.81[CEU][hapmap]
rs1425963	0.81[CEU][hapmap]
rs28490930	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1031603	chr4:187636716-188020741	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880401	chr4:187668795-188047143	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1015893	chr4:187768295-188338413	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv537441	chr4:187768295-188338413	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv525720	chr4:187792665-188426129	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv949342	chr4:187812637-188210592	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv1810466	chr4:187843890-187894950	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv880387	chr4:187845057-187943614	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1034395	chr4:187848064-188099748	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv537442	chr4:187848064-188099748	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv881568	chr4:187848075-188237194	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv508341	chr4:187849139-187895993	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1031606	chr4:187851202-188095665	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv537443	chr4:187851202-188095665	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1024709	chr4:187851202-188399934	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv1032747	chr4:187851202-188435238	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv1029517	chr4:187852818-188098962	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1030674	chr4:187852818-188449087	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	nsv432686	chr4:187856851-187878165	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv34733	chr4:187857192-187878165	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv534444	chr4:187857833-188511099	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
27	nsv532746	chr4:187857833-188573656	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
28	nsv1018032	chr4:187859265-187879695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv537444	chr4:187859265-187879695	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv880738	chr4:187860363-187894710	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv2763426	chr4:187861049-187878593	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv441934	chr4:187862193-187878503	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv4648	chr4:187863640-187901342	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
34	esv34947	chr4:187865835-187878165	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	esv2829838	chr4:187866343-187871454	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1863408	ZFP42	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187858600-187874800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:187862000-187870000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:187864800-187874400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:187865400-187870200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:187866800-187872200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:187867200-187870000	Enhancers	Liver	Liver
7	chr4:187868000-187874000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:187868200-187870400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:187868400-187880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:187869400-187870000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:187869400-187870200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:187869400-187870600	Flanking Active TSS	HSMMtube	muscle
13	chr4:187869400-187870600	Enhancers	NH-A	brain
14	chr4:187869600-187870000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:187869600-187870000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:187869600-187870000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:187869600-187870000	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr4:187869600-187870000	Flanking Active TSS	NHDF-Ad	bronchial
19	chr4:187869600-187870200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:187869600-187870200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr4:187869600-187870200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:187869600-187870200	Enhancers	Fetal Kidney	kidney
23	chr4:187869600-187870200	Enhancers	NHEK	skin
24	chr4:187869600-187870200	Flanking Active TSS	Osteobl	bone
25	chr4:187869600-187870600	Enhancers	Fetal Muscle Trunk	muscle
26	chr4:187869600-187870600	Enhancers	Fetal Stomach	stomach
27	chr4:187869600-187870600	Flanking Active TSS	HSMM	muscle
28	chr4:187869600-187871000	Enhancers	Pancreas	Pancrea
29	chr4:187869600-187871000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr4:187869600-187871200	Enhancers	Fetal Muscle Leg	muscle
31	chr4:187869800-187870000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr4:187869800-187870000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:187869800-187870000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:187869800-187870000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:187869800-187870000	Enhancers	Brain Germinal Matrix	brain
36	chr4:187869800-187870000	Enhancers	Fetal Heart	heart
37	chr4:187869800-187870000	Active TSS	Stomach Smooth Muscle	stomach
38	chr4:187869800-187870200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:187869800-187870200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:187869800-187870200	Enhancers	Duodenum Mucosa	Duodenum
41	chr4:187869800-187870200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr4:187869800-187870200	Flanking Active TSS	Fetal Lung	lung
43	chr4:187869800-187870200	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr4:187869800-187870200	Flanking Active TSS	NHLF	lung
45	chr4:187869800-187870400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:187869800-187870400	Enhancers	Placenta	Placenta
47	chr4:187869800-187870600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:187869800-187870600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr4:187869800-187870600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:187869800-187870600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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