Variant report

Variant	rs3845397
Chromosome Location	chr1:180240752-180240753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180199812..180202263-chr1:180239258..180241865,2	MCF-7	breast:
2	chr1:180197053..180202321-chr1:180236654..180241118,5	MCF-7	breast:
3	chr1:180239113..180241283-chr1:180242753..180244604,3	MCF-7	breast:
4	chr1:180239151..180242190-chr1:180245057..180248684,4	MCF-7	breast:
5	chr1:180239913..180241784-chr1:180250464..180252732,2	K562	blood:
6	chr1:180224817..180227850-chr1:180239195..180241654,3	MCF-7	breast:
7	chr1:180240013..180241625-chr1:180243549..180246315,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121454	Chromatin interaction
ENSG00000230124	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1043744	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494527	0.80[MKK][hapmap]
rs10798762	0.80[MKK][hapmap]
rs2290478	0.90[MEX][hapmap]
rs2296378	0.80[CHD][hapmap];0.82[GIH][hapmap]
rs4076403	0.80[MKK][hapmap]
rs4578179	0.80[MKK][hapmap]
rs716760	0.83[ASW][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.87[MKK][hapmap]
rs7536561	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1005512	chr1:180127616-180242659	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3845397	LHX4	cis	Thyroid	GTEx
rs3845397	RINT1	trans	cerebellum	SCAN
rs3845397	TEDDM1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180231000-180257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180232200-180242200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:180234200-180241400	Weak transcription	Primary T cells from cord blood	blood
4	chr1:180234400-180243000	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:180234800-180241400	Weak transcription	Primary B cells from cord blood	blood
6	chr1:180236000-180242400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:180236200-180252200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:180236400-180241400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:180236400-180241400	Enhancers	HSMMtube	muscle
10	chr1:180236400-180242200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:180236400-180249800	Weak transcription	Hela-S3	cervix
12	chr1:180236600-180242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:180236600-180243400	Weak transcription	Spleen	Spleen
14	chr1:180236800-180243000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:180236800-180257600	Weak transcription	Fetal Brain Male	brain
16	chr1:180237000-180241200	Enhancers	Fetal Muscle Leg	muscle
17	chr1:180237000-180241400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:180237000-180243000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:180237000-180243000	Weak transcription	Fetal Lung	lung
20	chr1:180237200-180241200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:180237200-180241400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:180237200-180241600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:180237200-180243200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:180237200-180243800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:180237400-180240800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:180237400-180241200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:180237400-180241800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:180237400-180242000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr1:180237400-180242200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:180237600-180242000	Weak transcription	Lung	lung
31	chr1:180237600-180243400	Weak transcription	Esophagus	oesophagus
32	chr1:180237800-180245000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:180238000-180241400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:180238000-180243800	Weak transcription	Fetal Kidney	kidney
35	chr1:180238400-180242200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:180238400-180242400	Weak transcription	Thymus	Thymus
37	chr1:180238600-180241600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:180238600-180241600	Enhancers	Fetal Intestine Large	intestine
39	chr1:180238600-180242800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:180238600-180255600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:180238800-180242200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:180238800-180243000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:180239000-180241200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:180239000-180241200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:180239000-180241200	Enhancers	K562	blood
46	chr1:180239000-180241400	Enhancers	Fetal Muscle Trunk	muscle
47	chr1:180239000-180241600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:180239000-180241600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:180239000-180242400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:180239000-180244400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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