Variant report

Variant	rs12700624
Chromosome Location	chr7:25399600-25399601
allele	A/C
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	KAP1	chr7:25399087-25399798	U2OS	brain:	n/a	n/a
2	REST	chr7:25398989-25399979	H1-neurons	neurons:	n/a	chr7:25399545-25399552
3	POLR2A	chr7:25398951-25399874	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr7:25398988-25399971	H1-neurons	neurons:	n/a	n/a
5	REST	chr7:25398485-25400551	H1-neurons	neurons:	n/a	chr7:25400080-25400098 chr7:25399545-25399552

Variant related genes	Relation type
ENSG00000260951	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1002203	0.88[EUR][1000 genomes]
rs1015497	0.89[EUR][1000 genomes]
rs10807824	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764103	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11769627	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11972231	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981869	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670448	1.00[ASN][1000 genomes]
rs12672062	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700616	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12700617	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700618	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700619	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12700620	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700621	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700623	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700625	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700628	0.88[EUR][1000 genomes]
rs13221394	0.88[EUR][1000 genomes]
rs13310680	0.89[EUR][1000 genomes]
rs1988282	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1988283	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2188993	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4134095	0.81[EUR][1000 genomes]
rs6461862	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6461864	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953741	0.82[EUR][1000 genomes]
rs6964890	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7811651	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs929239	0.89[EUR][1000 genomes]
rs929240	0.89[EUR][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	nsv606424	chr7:24982529-25466521	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv887846	chr7:25371700-25407621	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25398000-25400400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:25398000-25401200	Enhancers	Fetal Muscle Leg	muscle
3	chr7:25398200-25400600	Enhancers	Fetal Stomach	stomach
4	chr7:25398400-25400600	Enhancers	Fetal Intestine Small	intestine
5	chr7:25398600-25400200	Enhancers	Primary T cells from cord blood	blood
6	chr7:25398600-25400200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr7:25398800-25399600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:25398800-25399800	Active TSS	Brain Anterior Caudate	brain
9	chr7:25398800-25400200	Flanking Active TSS	Fetal Brain Male	brain
10	chr7:25398800-25400400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr7:25399000-25399600	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr7:25399000-25399600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:25399000-25399800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr7:25399000-25399800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:25399000-25400200	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr7:25399000-25400600	Enhancers	Fetal Kidney	kidney
17	chr7:25399200-25399600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:25399200-25399600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr7:25399200-25399600	Enhancers	NH-A	brain
20	chr7:25399200-25399800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:25399200-25399800	Active TSS	Fetal Brain Female	brain
22	chr7:25399200-25400000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr7:25399200-25400400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr7:25399400-25399600	Flanking Active TSS	Fetal Lung	lung
25	chr7:25399400-25399800	Active TSS	Brain Angular Gyrus	brain
26	chr7:25399400-25399800	Active TSS	Brain Germinal Matrix	brain
27	chr7:25399400-25399800	Active TSS	Brain Hippocampus Middle	brain
28	chr7:25399400-25399800	Active TSS	Brain Substantia Nigra	brain
29	chr7:25399400-25400600	Enhancers	Duodenum Mucosa	Duodenum
30	chr7:25399400-25400600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr7:25399600-25400600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:25399600-25400600	Enhancers	Fetal Lung	lung
33	chr7:25399600-25401200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr7:25399600-25401200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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