Variant report

Variant	rs6770643
Chromosome Location	chr3:196090469-196090470
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196068603..196070479-chr3:196087744..196090731,2	K562	blood:
2	chr3:196054797..196056651-chr3:196089177..196091738,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11185525	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11185536	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11185538	0.85[ASN][1000 genomes]
rs11707862	0.88[ASN][1000 genomes]
rs11713005	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11715772	0.88[ASN][1000 genomes]
rs11718924	0.88[ASN][1000 genomes]
rs12487829	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6770487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799210	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	esv3401011	chr3:196086397-196090496	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6770643	RNF168	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196054600-196091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:196070600-196106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:196071800-196100800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:196072400-196099600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:196074200-196099000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:196074800-196099000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:196077000-196100400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:196077800-196093200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:196077800-196095200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:196078800-196095000	Strong transcription	Fetal Muscle Leg	muscle
12	chr3:196079600-196090800	Strong transcription	Fetal Intestine Large	intestine
13	chr3:196079800-196091400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:196079800-196096800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:196079800-196099000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:196080000-196090600	Strong transcription	Placenta	Placenta
17	chr3:196080000-196090600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:196080000-196091400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:196080000-196093400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:196080200-196090600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:196080400-196090600	Strong transcription	Fetal Thymus	thymus
22	chr3:196080600-196090800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:196080600-196095000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:196080600-196100800	Strong transcription	Dnd41	blood
25	chr3:196080800-196090800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:196080800-196090800	Strong transcription	Ovary	ovary
27	chr3:196080800-196092600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:196081000-196090800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:196081000-196090800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:196081000-196091600	Strong transcription	GM12878-XiMat	blood
31	chr3:196081000-196094600	Strong transcription	HepG2	liver
32	chr3:196081200-196090800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:196081200-196099200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:196081800-196091000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:196081800-196091200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:196082000-196090800	Strong transcription	Thymus	Thymus
37	chr3:196082000-196099200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:196082200-196090600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:196082400-196090600	Strong transcription	Left Ventricle	heart
40	chr3:196082400-196090600	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:196082600-196091000	Strong transcription	Fetal Stomach	stomach
42	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
43	chr3:196083800-196092800	Weak transcription	Fetal Heart	heart
44	chr3:196083800-196094200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:196083800-196106400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:196084200-196100000	Strong transcription	Fetal Intestine Small	intestine
47	chr3:196084600-196131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:196085000-196093400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:196085200-196102200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:196085600-196091400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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