Variant report

Variant	rs12631199
Chromosome Location	chr3:112872821-112872822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr3:112872765-112872866	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112872686..112875261-chr3:112875839..112878613,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240057	TF binding region
ENSG00000240057	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10934222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934223	0.81[EUR][1000 genomes]
rs10934224	0.81[EUR][1000 genomes]
rs11712319	0.85[ASN][1000 genomes]
rs11716722	0.85[ASN][1000 genomes]
rs11720141	0.85[ASN][1000 genomes]
rs11923603	0.93[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs12490566	0.82[ASN][1000 genomes]
rs12631163	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634099	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2178398	0.85[ASN][1000 genomes]
rs2204788	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2204789	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2700229	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732812	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4528911	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4555493	0.85[ASN][1000 genomes]
rs62262801	0.85[ASN][1000 genomes]
rs62264166	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264172	0.81[EUR][1000 genomes]
rs6770160	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855348	0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12631199	BTLA	cis	parietal	SCAN
rs12631199	SIDT1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112867800-112873200	Enhancers	Rectal Smooth Muscle	rectum
2	chr3:112868000-112873400	Enhancers	Colon Smooth Muscle	Colon
3	chr3:112868200-112874400	Weak transcription	Placenta	Placenta
4	chr3:112869000-112873000	Enhancers	Fetal Kidney	kidney
5	chr3:112869600-112874600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:112870000-112873000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:112870000-112873200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:112870200-112873000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:112871000-112876600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:112871000-112881400	Weak transcription	Fetal Lung	lung
11	chr3:112871400-112873000	Enhancers	HSMMtube	muscle
12	chr3:112871400-112875800	Weak transcription	Fetal Stomach	stomach
13	chr3:112871400-112876000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:112871400-112876000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:112871600-112873200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:112871600-112875200	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:112871800-112873000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:112872000-112873000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:112872000-112873000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:112872000-112873000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:112872000-112873000	Enhancers	HSMM	muscle
22	chr3:112872000-112873400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:112872200-112873000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:112872200-112873000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:112872200-112873000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:112872200-112873000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:112872200-112873000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr3:112872200-112873000	Flanking Active TSS	GM12878-XiMat	blood
29	chr3:112872400-112873000	Enhancers	HMEC	breast
30	chr3:112872400-112876000	Weak transcription	Adipose Nuclei	Adipose
31	chr3:112872600-112873000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr3:112872600-112873000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:112872600-112873000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:112872600-112873000	Enhancers	A549	lung
35	chr3:112872800-112873000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:112872800-112873200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:112872800-112873200	Enhancers	Osteobl	bone
38	chr3:112872800-112874600	Weak transcription	H1 Cell Line	embryonic stem cell

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