Variant report

Variant	rs2058683
Chromosome Location	chr2:37012135-37012136
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37011366..37014092-chr2:37310068..37313025,2	K562	blood:
2	chr2:36579342..36579861-chr2:37012057..37012873,2	K562	blood:
3	chr2:36922543..36923508-chr2:37012076..37013001,3	MCF-7	breast:
4	chr2:37008165..37009704-chr2:37010243..37012241,2	MCF-7	breast:
5	chr2:37005478..37008643-chr2:37010810..37013126,3	MCF-7	breast:
6	chr2:37006258..37010448-chr2:37010681..37014372,3	K562	blood:

Variant related genes	Relation type
ENSG00000008869	Chromatin interaction
ENSG00000152133	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10200548	0.93[CHB][hapmap]
rs11124547	0.86[CHB][hapmap]
rs11892193	0.93[CHB][hapmap];0.88[GIH][hapmap]
rs11901202	0.85[CHB][hapmap]
rs11902881	0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap]
rs13417089	0.93[CHB][hapmap]
rs1558701	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17019813	1.00[TSI][hapmap]
rs17019851	0.88[GIH][hapmap];0.88[JPT][hapmap]
rs17019853	1.00[TSI][hapmap]
rs17019854	0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap]
rs2041809	0.85[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2058682	1.00[TSI][hapmap]
rs2072525	0.86[CHB][hapmap]
rs2072527	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs3821147	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4670169	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4670170	0.84[ASN][1000 genomes]
rs56740767	0.90[ASN][1000 genomes]
rs6544039	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6705145	1.00[TSI][hapmap]
rs7592382	0.91[CHB][hapmap]
rs7606098	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs763724	1.00[JPT][hapmap]
rs879613	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs879614	0.89[JPT][hapmap]
rs929640	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription 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	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1821275	chr2:36991736-37018278	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2058683	CRIM1	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37006000-37014600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:37007600-37012600	Weak transcription	Ovary	ovary
3	chr2:37007800-37012200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:37007800-37012200	Weak transcription	Liver	Liver
5	chr2:37007800-37012200	Weak transcription	Stomach Mucosa	stomach
6	chr2:37008200-37012200	Weak transcription	Fetal Heart	heart
7	chr2:37009800-37012400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:37009800-37016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:37010000-37012600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:37010000-37014000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:37010000-37016000	Weak transcription	Brain Anterior Caudate	brain
12	chr2:37010000-37021600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:37010400-37012200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:37010800-37012200	Weak transcription	Fetal Stomach	stomach
15	chr2:37010800-37012600	Weak transcription	Right Atrium	heart
16	chr2:37011200-37012400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:37011400-37012800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr2:37011400-37012800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr2:37011400-37013000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr2:37011400-37013200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:37011600-37013000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:37011800-37013000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:37012000-37012400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:37012000-37012400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:37012000-37012400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:37012000-37012600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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