Variant report

Variant	rs11682175
Chromosome Location	chr2:57987593-57987594
allele	C/T
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	BATF	chr2:57987544-57987875	GM12878	blood:	n/a	n/a
2	IKZF1	chr2:57987410-57987953	GM12878	blood:	n/a	n/a
3	MXI1	chr2:57987015-57987965	GM12878	blood:	n/a	n/a
4	RAD21	chr2:57986847-57987810	H1-hESC	embryonic stem cell:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
5	EBF1	chr2:57987043-57987925	GM12878	blood:	n/a	n/a
6	WRNIP1	chr2:57987032-57987834	GM12878	blood:	n/a	n/a
7	RAD21	chr2:57986938-57987968	GM12878	blood:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
8	RCOR1	chr2:57986975-57987893	GM12878	blood:	n/a	n/a
9	CTCF	chr2:57986812-57987611	HCT-116	colon:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
10	RAD21	chr2:57986882-57987597	HCT-116	colon:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
11	MAX	chr2:57986883-57987641	A549	lung:	n/a	n/a
12	MAX	chr2:57986990-57987627	A549	lung:	n/a	n/a
13	EP300	chr2:57987007-57987930	GM12878	blood:	n/a	chr2:57987675-57987684
14	CTCF	chr2:57986623-57988126	A549	lung:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
15	NFIC	chr2:57986921-57988035	GM12878	blood:	n/a	n/a
16	TCF12	chr2:57986771-57987746	A549	lung:	n/a	chr2:57987117-57987124 chr2:57987119-57987126
17	SMC3	chr2:57986732-57988020	GM12878	blood:	n/a	chr2:57987139-57987153
18	RAD21	chr2:57986800-57987641	A549	lung:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
19	RUNX3	chr2:57986990-57988002	GM12878	blood:	n/a	n/a
20	RAD21	chr2:57986870-57987950	GM12878	blood:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
21	IRF4	chr2:57987513-57987911	GM12878	blood:	n/a	n/a
22	RUNX3	chr2:57986993-57988058	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:57986735..57987942-chr2:58674900..58675939,5	MCF-7	breast:
2	chr2:57986795..57987623-chr2:58674835..58675860,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271615	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1106090	0.80[MEX][hapmap]
rs11688767	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11695135	0.89[ASN][1000 genomes]
rs1568452	0.86[ASN][1000 genomes]
rs2717046	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874197	chr2:57978858-58068741	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834148	chr2:57979661-58119213	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv874198	chr2:57987593-58068741	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11682175	SOCS4	trans	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57985400-57988400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:57986200-57987800	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:57986200-57987800	Enhancers	Duodenum Smooth Muscle	Duodenum
4	chr2:57986400-57987800	Active TSS	Brain Substantia Nigra	brain
5	chr2:57986400-57988000	Active TSS	Brain Angular Gyrus	brain
6	chr2:57986600-57987600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:57986600-57987600	Bivalent Enhancer	Stomach Mucosa	stomach
8	chr2:57986600-57988000	Active TSS	Brain Cingulate Gyrus	brain
9	chr2:57986600-57988000	Enhancers	Fetal Lung	lung
10	chr2:57986800-57987600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:57986800-57987600	Active TSS	Brain Hippocampus Middle	brain
12	chr2:57986800-57987600	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr2:57986800-57987600	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:57986800-57987600	Flanking Active TSS	Osteobl	bone
15	chr2:57986800-57987800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:57986800-57987800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:57986800-57987800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr2:57986800-57987800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:57986800-57987800	Enhancers	Fetal Heart	heart
20	chr2:57986800-57987800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr2:57987000-57987600	Active TSS	Primary T cells from cord blood	blood
22	chr2:57987000-57987600	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr2:57987000-57987800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:57987000-57987800	Enhancers	Primary B cells from cord blood	blood
25	chr2:57987000-57987800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr2:57987000-57987800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:57987000-57987800	Active TSS	Brain Anterior Caudate	brain
28	chr2:57987200-57987600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:57987200-57987600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
30	chr2:57987200-57987600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:57987200-57987600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:57987200-57987600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:57987200-57987600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr2:57987200-57987600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:57987200-57987600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:57987200-57987600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:57987200-57987600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr2:57987200-57987600	Active TSS	Colonic Mucosa	Colon
39	chr2:57987200-57987600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr2:57987200-57987600	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr2:57987200-57987600	Flanking Active TSS	Fetal Thymus	thymus
42	chr2:57987200-57987600	Enhancers	Right Ventricle	heart
43	chr2:57987200-57987600	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr2:57987200-57987600	Flanking Active TSS	HUVEC	blood vessel
45	chr2:57987200-57987600	Active TSS	NHDF-Ad	bronchial
46	chr2:57987200-57987800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:57987200-57987800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:57987200-57987800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr2:57987200-57987800	Flanking Active TSS	Fetal Brain Male	brain
50	chr2:57987200-57987800	Enhancers	Fetal Intestine Large	intestine

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