Variant report

Variant	rs9846106
Chromosome Location	chr3:196126539-196126540
allele	A/G
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	POLR2A	chr3:196126514-196126618	ProgFib	skin:	n/a	n/a
2	GATA1	chr3:196126364-196127125	PBDE	blood:	n/a	n/a
3	FOSL1	chr3:196126460-196127049	HCT-116	colon:	n/a	n/a
4	JUND	chr3:196126469-196126988	SK-N-SH	brain:	n/a	chr3:196126719-196126730
5	TCF7L2	chr3:196126466-196126979	Hela-S3	cervix:	n/a	n/a
6	PBX3	chr3:196126438-196127029	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr3:196126372-196126970	SK-N-SH	brain:	n/a	n/a
8	JUND	chr3:196126387-196127053	SK-N-SH	brain:	n/a	chr3:196126719-196126730
9	EP300	chr3:196126437-196127060	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:196126472-196126888	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr3:196126451-196127042	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr3:196126298-196126986	SK-N-SH	brain:	n/a	n/a
13	FOSL2	chr3:196126492-196126876	A549	lung:	n/a	n/a
14	GATA3	chr3:196126307-196127081	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr3:196126370-196126984	SK-N-SH	brain:	n/a	n/a
16	NFIC	chr3:196126439-196126957	SK-N-SH	brain:	n/a	n/a
17	USF2	chr3:196126452-196126942	Hela-S3	cervix:	n/a	n/a
18	JUND	chr3:196126473-196127042	SK-N-SH	brain:	n/a	chr3:196126719-196126730
19	FOSL2	chr3:196126510-196126966	MCF-7	breast:	n/a	n/a
20	RCOR1	chr3:196126466-196126920	Hela-S3	cervix:	n/a	n/a
21	USF1	chr3:196126267-196126550	K562	blood:	n/a	n/a
22	BHLHE40	chr3:196126286-196126617	K562	blood:	n/a	n/a
23	JUND	chr3:196126518-196126910	Hela-S3	cervix:	n/a	chr3:196126719-196126730
24	TAL1	chr3:196126463-196126696	K562	blood:	n/a	n/a
25	MAX	chr3:196126339-196126955	Hela-S3	cervix:	n/a	n/a
26	TCF12	chr3:196126334-196127059	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196119980..196121933-chr3:196124713..196127635,2	K562	blood:
2	chr3:196068585..196071026-chr3:196125432..196127097,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL434P	TF binding region
RN7SL738P	TF binding region
ENSG00000212146	Chromatin interaction
ENSG00000206644	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12637868	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28712197	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34801745	0.99[ASN][1000 genomes]
rs35959625	1.00[ASN][1000 genomes]
rs3973	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459932	0.96[ASN][1000 genomes]
rs4577498	0.88[ASN][1000 genomes]
rs4916427	0.82[EUR][1000 genomes]
rs4916492	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916493	0.89[ASN][1000 genomes]
rs61345811	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6583305	0.86[ASN][1000 genomes]
rs6774894	0.99[ASN][1000 genomes]
rs7372674	0.90[ASN][1000 genomes]
rs7618690	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9867369	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	esv32642	chr3:196118819-196153861	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9846106	UBXD7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
3	chr3:196084600-196131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
5	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
6	chr3:196098000-196126800	Weak transcription	Pancreas	Pancrea
7	chr3:196113200-196136400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:196115400-196127800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:196115400-196127800	Strong transcription	Placenta	Placenta
10	chr3:196115400-196127800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:196115400-196129800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:196115600-196134600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:196116200-196126800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:196116200-196129200	Strong transcription	Fetal Stomach	stomach
15	chr3:196116200-196134000	Strong transcription	Fetal Intestine Small	intestine
16	chr3:196116600-196131800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:196116600-196133600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:196117200-196126600	Weak transcription	Gastric	stomach
19	chr3:196117200-196126800	Weak transcription	Right Ventricle	heart
20	chr3:196117800-196127800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:196117800-196131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:196118000-196133600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:196118000-196134800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:196118800-196130400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:196118800-196133600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:196118800-196136000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:196119000-196126600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:196119200-196126800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:196119200-196127000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:196119400-196126800	Weak transcription	Lung	lung
32	chr3:196120400-196130800	Strong transcription	GM12878-XiMat	blood
33	chr3:196120400-196133600	Weak transcription	Fetal Brain Male	brain
34	chr3:196121400-196134000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:196121600-196127600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr3:196122400-196127600	Strong transcription	Thymus	Thymus
37	chr3:196122400-196128000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:196122400-196130200	Strong transcription	Fetal Intestine Large	intestine
39	chr3:196122400-196130600	Strong transcription	Fetal Thymus	thymus
40	chr3:196122400-196134200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:196123400-196128000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:196123400-196134000	Strong transcription	Primary B cells from cord blood	blood
43	chr3:196123600-196127800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:196123800-196127600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:196123800-196127800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:196123800-196127800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:196123800-196128000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:196123800-196128000	Strong transcription	Adipose Nuclei	Adipose
49	chr3:196123800-196129400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr3:196123800-196129600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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