Variant report

Variant	rs34992220
Chromosome Location	chr3:136468637-136468638
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	ZNF384	chr3:136468426-136468832	GM12878	blood:	n/a	n/a
2	TCF7L2	chr3:136468447-136469700	HEK293	kidney:	n/a	chr3:136469328-136469335
3	GATA1	chr3:136468374-136470431	PBDE	blood:	n/a	chr3:136470275-136470286 chr3:136470111-136470120 chr3:136469391-136469407 chr3:136470108-136470124 chr3:136469393-136469405
4	RCOR1	chr3:136468552-136468790	K562	blood:	n/a	n/a
5	RCOR1	chr3:136468484-136468865	K562	blood:	n/a	n/a
6	ZNF384	chr3:136467785-136468805	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136466613..136474326-chr3:136579481..136583133,10	K562	blood:
2	chr3:136208388..136211090-chr3:136467197..136470066,2	K562	blood:
3	chr3:136261604..136263396-chr3:136467886..136469461,2	K562	blood:
4	chr3:136233567..136235148-chr3:136468458..136469958,2	K562	blood:
5	chr3:136389263..136391478-chr3:136467252..136469430,2	K562	blood:
6	chr3:136444891..136447189-chr3:136467226..136469420,2	K562	blood:

Variant related genes	Relation type
ENSG00000261758	TF binding region
ENSG00000158092	Chromatin interaction
ENSG00000239213	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10155016	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10155017	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10513014	0.95[CEU][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12107125	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12630999	0.87[CHD][hapmap]
rs12635723	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs13433980	0.86[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs1484250	0.86[CEU][hapmap];0.85[YRI][hapmap]
rs1681817	0.92[JPT][hapmap]
rs28452147	0.81[ASN][1000 genomes]
rs28489907	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3856637	0.87[CHD][hapmap]
rs4336059	0.82[CEU][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs4678437	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs4678438	0.92[CHD][hapmap]
rs61322732	0.88[ASN][1000 genomes]
rs61508594	0.88[ASN][1000 genomes]
rs61790842	0.88[ASN][1000 genomes]
rs6439656	0.91[ASN][1000 genomes]
rs6765239	0.86[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap]
rs6771713	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs6782151	0.82[CEU][hapmap];0.94[MEX][hapmap];0.85[YRI][hapmap]
rs6789329	0.83[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6794351	0.87[CHD][hapmap]
rs6795227	0.91[ASN][1000 genomes]
rs6799699	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs6800969	0.86[CEU][hapmap];0.89[YRI][hapmap]
rs6808312	0.90[CHB][hapmap]
rs7612160	0.82[CEU][hapmap];0.94[MEX][hapmap]
rs7623824	0.84[ASW][hapmap];0.82[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs7644346	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs7644471	0.81[CEU][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.89[YRI][hapmap]
rs9812541	0.86[ASN][1000 genomes]
rs9813590	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813596	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9820513	0.86[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs9821478	1.00[JPT][hapmap]
rs9833207	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9839574	0.86[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs9845762	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9845950	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs9853960	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869957	0.86[CEU][hapmap];0.88[YRI][hapmap]
rs9871160	0.87[ASN][1000 genomes]

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	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136449000-136470000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:136450800-136469000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:136454200-136469200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:136454200-136470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:136454400-136469200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:136454800-136469200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:136457400-136470000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:136458400-136470000	Weak transcription	Esophagus	oesophagus
9	chr3:136463800-136468800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:136464400-136469000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:136465800-136470000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:136466600-136469200	Weak transcription	Placenta	Placenta
13	chr3:136467000-136469000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:136467200-136468800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:136467200-136469000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:136467400-136469000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr3:136467400-136469000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:136467400-136469000	Enhancers	Right Ventricle	heart
19	chr3:136467400-136469200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:136467600-136468800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:136467600-136468800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:136467600-136468800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr3:136467600-136468800	Enhancers	HepG2	liver
24	chr3:136467600-136469000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr3:136467600-136469000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr3:136467600-136469000	Enhancers	Brain Germinal Matrix	brain
27	chr3:136467600-136469000	Enhancers	Left Ventricle	heart
28	chr3:136467600-136469200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:136467600-136469200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:136467600-136469200	Enhancers	Fetal Heart	heart
31	chr3:136467800-136468800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:136467800-136468800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:136467800-136468800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:136467800-136468800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:136467800-136468800	Enhancers	Brain Hippocampus Middle	brain
36	chr3:136467800-136469000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:136467800-136469000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:136467800-136469000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:136467800-136469000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:136467800-136469000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr3:136467800-136469000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:136467800-136469000	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr3:136467800-136469000	Enhancers	Primary B cells from cord blood	blood
44	chr3:136467800-136469000	Enhancers	Primary T cells from cord blood	blood
45	chr3:136467800-136469000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:136467800-136469000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:136467800-136469000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:136467800-136469000	Enhancers	Adipose Nuclei	Adipose
49	chr3:136467800-136469000	Enhancers	Liver	Liver
50	chr3:136467800-136469000	Enhancers	Brain Anterior Caudate	brain

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