Variant report

Variant	rs3007680
Chromosome Location	chr1:152016425-152016426
allele	A/G
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	chr1:152015038..152017960-chr1:152041369..152043398,2	K562	blood:
2	chr1:151880046..151882777-chr1:152015167..152017625,2	MCF-7	breast:
3	chr1:152004043..152013121-chr1:152013584..152022966,19	K562	blood:
4	chr1:152014558..152016795-chr5:154161907..154163941,2	MCF-7	breast:
5	chr1:152014593..152017230-chr1:152082456..152084502,3	MCF-7	breast:
6	chr1:152015810..152018390-chr1:152153370..152155715,2	K562	blood:
7	chr1:152013400..152016839-chr1:152017055..152020661,5	K562	blood:
8	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1131471	0.82[JPT][hapmap]
rs1496036	0.82[JPT][hapmap]
rs2069258	0.86[JPT][hapmap]
rs2496253	0.82[JPT][hapmap]
rs2935208	0.81[JPT][hapmap]
rs2999563	0.84[JPT][hapmap]
rs3001978	0.82[JPT][hapmap]
rs3124316	0.95[CEU][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4579760	0.82[JPT][hapmap]
rs4845419	0.82[JPT][hapmap]
rs4845420	0.81[JPT][hapmap]
rs924087	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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 target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
5	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3007680	THEM4	cis	cerebellum	SCAN
rs3007680	RORC	cis	parietal	SCAN
rs3007680	SCNM1	cis	parietal	SCAN
rs3007680	LCE3A	cis	parietal	SCAN
rs3007680	LCE2D	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152009600-152019800	Weak transcription	Small Intestine	intestine
2	chr1:152010000-152017000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:152010000-152018400	Weak transcription	A549	lung
4	chr1:152010000-152018400	Weak transcription	NHEK	skin
5	chr1:152010000-152019800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:152010000-152020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:152010200-152020000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:152010200-152020000	Weak transcription	Colonic Mucosa	Colon
9	chr1:152010200-152020400	Weak transcription	Gastric	stomach
10	chr1:152010800-152018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:152011400-152019600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:152012600-152019200	Weak transcription	Esophagus	oesophagus
13	chr1:152012800-152019600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:152012800-152019600	Weak transcription	Thymus	Thymus
15	chr1:152013200-152018600	Weak transcription	K562	blood
16	chr1:152014000-152018800	Weak transcription	Stomach Mucosa	stomach
17	chr1:152014400-152016600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:152015000-152019000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:152015200-152018200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:152015400-152018000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:152015600-152017800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:152015600-152018000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:152015800-152017000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:152016000-152016800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:152016000-152016800	Enhancers	Fetal Intestine Large	intestine
26	chr1:152016000-152017400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:152016000-152017400	Enhancers	Fetal Thymus	thymus
28	chr1:152016000-152018000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:152016000-152018000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr1:152016000-152018400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:152016000-152020000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:152016000-152020000	Enhancers	Placenta	Placenta
33	chr1:152016200-152016600	Enhancers	Fetal Intestine Small	intestine
34	chr1:152016200-152016800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:152016200-152017200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:152016200-152017400	Enhancers	HMEC	breast
37	chr1:152016200-152017800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:152016200-152018000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:152016200-152018000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:152016400-152016800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:152016400-152016800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:152016400-152017400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:152016400-152017400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr1:152016400-152017400	Enhancers	Hela-S3	cervix
45	chr1:152016400-152017600	Enhancers	Adipose Nuclei	Adipose

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