Variant report

Variant	rs3931977
Chromosome Location	chr8:103209964-103209965
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:102503403..102505904-chr8:103208888..103211363,2	MCF-7	breast:
2	chr8:102658165..102659183-chr8:103208962..103210318,7	MCF-7	breast:
3	chr8:103044931..103046316-chr8:103209230..103210787,8	MCF-7	breast:
4	chr8:103204658..103207818-chr8:103209461..103212038,3	K562	blood:
5	chr8:102338887..102339423-chr8:103209592..103210278,2	K562	blood:
6	chr8:102619068..102621889-chr8:103209199..103211504,2	MCF-7	breast:
7	chr8:102339044..102339677-chr8:103209457..103210233,4	MCF-7	breast:
8	chr8:102345252..102346969-chr8:103208842..103210434,2	MCF-7	breast:
9	chr8:102671400..102672173-chr8:103209393..103210217,2	MCF-7	breast:
10	chr8:103208196..103211132-chr8:103214844..103217126,2	K562	blood:
11	chr8:102658241..102659174-chr8:103209354..103210263,6	MCF-7	breast:
12	chr8:102513354..102514192-chr8:103209647..103210273,2	MCF-7	breast:
13	chr8:103045077..103045953-chr8:103209208..103210205,5	MCF-7	breast:
14	chr8:102313542..102314283-chr8:103209426..103210117,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000083307	Chromatin interaction
ENSG00000254024	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12114277	0.83[MEX][hapmap]
rs1265147	0.81[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2607657	0.81[ASN][1000 genomes]
rs2607658	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs2607659	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2607662	0.83[MEX][hapmap]
rs2853229	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs2853233	0.83[MEX][hapmap]
rs4102400	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6468819	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6980902	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3931977	CTHRC1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103209000-103210000	Enhancers	Primary B cells from peripheral blood	blood
2	chr8:103209200-103210000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr8:103209200-103210600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:103209200-103210600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:103209200-103210600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:103209200-103210600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr8:103209200-103210800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr8:103209400-103210200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:103209400-103210200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr8:103209400-103210200	Enhancers	Fetal Brain Male	brain
11	chr8:103209400-103210600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:103209600-103210000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:103209600-103210600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr8:103209600-103210600	Enhancers	Fetal Muscle Trunk	muscle
15	chr8:103209600-103218400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:103209600-103223000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr8:103209800-103210000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr8:103209800-103210000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:103209800-103210000	Enhancers	Brain Angular Gyrus	brain
20	chr8:103209800-103210000	Enhancers	Brain Hippocampus Middle	brain
21	chr8:103209800-103210000	Enhancers	Duodenum Mucosa	Duodenum
22	chr8:103209800-103210000	Enhancers	Fetal Thymus	thymus
23	chr8:103209800-103210000	Enhancers	Ovary	ovary
24	chr8:103209800-103210000	Enhancers	Psoas Muscle	Psoas
25	chr8:103209800-103210000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr8:103209800-103210000	Bivalent Enhancer	Dnd41	blood
27	chr8:103209800-103210200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:103209800-103210200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr8:103209800-103210200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr8:103209800-103210200	Enhancers	Stomach Smooth Muscle	stomach
31	chr8:103209800-103210400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:103209800-103210400	Enhancers	Fetal Stomach	stomach
33	chr8:103209800-103210400	Enhancers	NHDF-Ad	bronchial
34	chr8:103209800-103210600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr8:103209800-103210600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr8:103209800-103210600	Enhancers	Fetal Muscle Leg	muscle
37	chr8:103209800-103210800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr8:103209800-103211000	Enhancers	Fetal Brain Female	brain
39	chr8:103209800-103211600	Flanking Active TSS	GM12878-XiMat	blood
40	chr8:103209800-103216200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:103209800-103216400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr8:103209800-103216400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr8:103209800-103217200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr8:103209800-103217800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:103209800-103218000	Weak transcription	Adipose Nuclei	Adipose
46	chr8:103209800-103218400	Weak transcription	HMEC	breast
47	chr8:103209800-103218600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr8:103209800-103218600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr8:103209800-103218600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr8:103209800-103218800	Weak transcription	Primary B cells from cord blood	blood

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