Variant report

Variant	rs6544231
Chromosome Location	chr2:39711217-39711218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39692371..39695353-chr2:39710610..39713558,3	MCF-7	breast:
2	chr2:39709054..39711333-chr2:39713452..39715456,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10183115	1.00[CEU][hapmap]
rs13398961	1.00[CEU][hapmap]
rs13410300	1.00[CEU][hapmap]
rs13414685	1.00[CEU][hapmap]
rs13414845	1.00[CEU][hapmap]
rs13415549	1.00[ASN][1000 genomes]
rs13429046	1.00[ASN][1000 genomes]
rs13430261	1.00[CEU][hapmap]
rs1474424	1.00[MEX][hapmap]
rs28667057	1.00[ASN][1000 genomes]
rs4670934	1.00[MEX][hapmap]
rs6544223	1.00[MEX][hapmap]
rs7574785	1.00[MEX][hapmap]
rs7582160	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6544231	CRIM1	cis	cerebellum	SCAN
rs6544231	FAM82A1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39696600-39711600	Weak transcription	Fetal Brain Female	brain
2	chr2:39697200-39711400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:39697200-39711800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:39697200-39713200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:39697400-39715400	Weak transcription	Pancreas	Pancrea
6	chr2:39697400-39722000	Weak transcription	Fetal Stomach	stomach
7	chr2:39697400-39722000	Weak transcription	Right Ventricle	heart
8	chr2:39697400-39724200	Weak transcription	Gastric	stomach
9	chr2:39697600-39714600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:39697600-39714600	Weak transcription	Fetal Kidney	kidney
11	chr2:39702200-39726000	Weak transcription	Fetal Intestine Small	intestine
12	chr2:39703400-39713200	Weak transcription	HSMMtube	muscle
13	chr2:39705400-39711600	Weak transcription	Liver	Liver
14	chr2:39705400-39719400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:39705600-39711400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:39705600-39713000	Weak transcription	Placenta	Placenta
17	chr2:39705600-39715200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:39705600-39719000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:39705600-39721600	Weak transcription	Psoas Muscle	Psoas
20	chr2:39705800-39712000	Weak transcription	HepG2	liver
21	chr2:39705800-39713400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:39706000-39714400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39706200-39715400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:39706400-39711800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:39707400-39724200	Weak transcription	Fetal Brain Male	brain
26	chr2:39708200-39715400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:39709200-39711600	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:39709200-39711800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:39709200-39713200	Weak transcription	NHDF-Ad	bronchial
30	chr2:39709200-39714400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:39709400-39711600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:39709800-39714000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:39710000-39711400	Enhancers	Stomach Mucosa	stomach
34	chr2:39710000-39711600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr2:39710000-39711600	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:39710000-39712000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:39710000-39712600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:39710200-39711600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:39710200-39711600	Enhancers	NHLF	lung
40	chr2:39710200-39715200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:39710400-39711400	Enhancers	K562	blood
42	chr2:39710400-39711400	Enhancers	NH-A	brain
43	chr2:39710400-39712200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:39710400-39712400	Enhancers	Fetal Heart	heart
45	chr2:39710600-39711400	Flanking Active TSS	HUVEC	blood vessel
46	chr2:39710600-39711400	Enhancers	Osteobl	bone
47	chr2:39710600-39711600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:39710600-39711600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:39710600-39711600	Enhancers	HSMM	muscle
50	chr2:39710600-39712600	Enhancers	Adipose Nuclei	Adipose

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