Variant report

Variant	rs2233798
Chromosome Location	chr9:19048957-19048958
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	ATF3	chr9:19048911-19049452	A549	lung:	n/a	n/a
2	YY1	chr9:19048932-19050155	GM12878	blood:	n/a	chr9:19049080-19049091 chr9:19049579-19049590 chr9:19049617-19049631 chr9:19049452-19049466
3	RFX5	chr9:19048856-19049561	HepG2	liver:	n/a	chr9:19049204-19049219 chr9:19049207-19049216 chr9:19049205-19049219
4	MAX	chr9:19048713-19050204	HepG2	liver:	n/a	n/a
5	ZBTB33	chr9:19048832-19049746	SK-N-SH	brain:	n/a	chr9:19049356-19049366 chr9:19049358-19049367 chr9:19049359-19049369
6	POLR2A	chr9:19048930-19049662	A549	lung:	n/a	n/a
7	SMC3	chr9:19048802-19049817	Hela-S3	cervix:	n/a	chr9:19049164-19049178
8	USF2	chr9:19048887-19049375	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:19048867-19052986	Hela-S3	cervix:	n/a	n/a
10	NFIC	chr9:19048814-19050059	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:19048837-19050536	GM19193	blood:	n/a	n/a
12	GABPA	chr9:19048930-19049883	A549	lung:	n/a	n/a
13	MXI1	chr9:19048918-19050208	Hela-S3	cervix:	n/a	chr9:19049201-19049216
14	RAD21	chr9:19048920-19049371	A549	lung:	n/a	chr9:19049167-19049176 chr9:19049166-19049179 chr9:19049075-19049088 chr9:19049163-19049182
15	POLR2A	chr9:19048849-19050253	GM12891	blood:	n/a	n/a
16	POLR2A	chr9:19048626-19050275	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr9:19048860-19050025	GM12892	blood:	n/a	n/a
18	TAF1	chr9:19048704-19049635	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr9:19048707-19049669	ECC-1	luminal epithelium:	n/a	chr9:19049540-19049556 chr9:19048854-19048868 chr9:19049374-19049381 chr9:19049537-19049553
20	POU2F2	chr9:19048924-19049655	GM12891	blood:	n/a	chr9:19049588-19049600 chr9:19049383-19049395
21	REST	chr9:19048456-19050673	H1-neurons	neurons:	n/a	chr9:19049531-19049544 chr9:19049550-19049563 chr9:19049514-19049532 chr9:19049631-19049649 chr9:19049553-19049566
22	HCFC1	chr9:19048511-19050417	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr9:19048922-19049689	K562	blood:	n/a	n/a
24	POLR2A	chr9:19048797-19050701	GM12892	blood:	n/a	n/a
25	FOXM1	chr9:19048787-19049779	GM12878	blood:	n/a	n/a
26	POLR2A	chr9:19048838-19050762	MCF-7	breast:	n/a	n/a
27	REST	chr9:19048874-19049964	A549	lung:	n/a	chr9:19049531-19049544 chr9:19049550-19049563 chr9:19049514-19049532 chr9:19049631-19049649 chr9:19049553-19049566
28	MYC	chr9:19048938-19049523	MCF-7	breast:	n/a	n/a
29	YY1	chr9:19048933-19049841	A549	lung:	n/a	chr9:19049080-19049091 chr9:19049579-19049590 chr9:19049617-19049631 chr9:19049452-19049466
30	ATF2	chr9:19048920-19049758	GM12878	blood:	n/a	n/a
31	POLR2A	chr9:19048832-19049812	HUVEC	blood vessel:	n/a	n/a
32	JUND	chr9:19048920-19050125	K562	blood:	n/a	n/a
33	CTCF	chr9:19048868-19049415	MCF-7	breast:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
34	BRCA1	chr9:19048567-19050272	Hela-S3	cervix:	n/a	chr9:19049231-19049238 chr9:19049358-19049367
35	SIX5	chr9:19048864-19049558	A549	lung:	n/a	n/a
36	TAF1	chr9:19048830-19050163	H1-neurons	neurons:	n/a	n/a
37	E2F6	chr9:19048892-19049918	K562	blood:	n/a	chr9:19049751-19049763 chr9:19049547-19049556
38	TBP	chr9:19048873-19049637	HepG2	liver:	n/a	n/a
39	EP300	chr9:19048869-19049513	GM12878	blood:	n/a	chr9:19049374-19049381
40	RCOR1	chr9:19048591-19050122	Hela-S3	cervix:	n/a	n/a
41	SP1	chr9:19048849-19049607	A549	lung:	n/a	chr9:19049338-19049350 chr9:19049338-19049350 chr9:19049587-19049601
42	CTCF	chr9:19048842-19049434	GM12878	blood:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
43	STAT3	chr9:19048575-19049377	GM12878	blood:	n/a	n/a
44	HMGN3	chr9:19048908-19049759	K562	blood:	n/a	n/a
45	CTCF	chr9:19048858-19049546	K562	blood:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
46	ELF1	chr9:19048900-19049548	HepG2	liver:	n/a	n/a
47	HDAC2	chr9:19048925-19049461	HepG2	liver:	n/a	n/a
48	ZEB1	chr9:19048792-19049454	GM12878	blood:	n/a	n/a
49	GATA3	chr9:19048852-19049858	A549	lung:	n/a	n/a
50	TAF1	chr9:19048852-19049769	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:19048422..19049254-chr9:19457178..19458008,3	K562	blood:
2	chr9:19047624..19049710-chr9:19124952..19127835,2	MCF-7	breast:
3	chr9:19048660..19050563-chr9:19101012..19103938,3	MCF-7	breast:
4	chr9:19047048..19050954-chr9:19228997..19232024,5	K562	blood:
5	chr9:19047789..19050837-chr9:19378682..19381375,3	MCF-7	breast:
6	chr9:19048684..19049542-chr9:100684339..100685327,2	Hela-S3	cervix:
7	chr9:19047688..19050062-chr9:19125989..19129041,3	K562	blood:
8	chr9:19032362..19034123-chr9:19046838..19049376,2	MCF-7	breast:

Variant related genes	Relation type
RRAGA	TF binding region
ENSG00000147872	Chromatin interaction
ENSG00000147874	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000137154	Chromatin interaction
ENSG00000155875	Chromatin interaction
ENSG00000137145	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10122990	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10123400	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10123624	0.84[ASN][1000 genomes]
rs10125646	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125677	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1048169	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10757024	0.86[ASN][1000 genomes]
rs10757025	0.86[ASN][1000 genomes]
rs10811103	0.83[ASN][1000 genomes]
rs10811104	0.86[ASN][1000 genomes]
rs10811107	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10811108	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10963921	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10963924	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10963925	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10963942	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1154672	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1154673	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12236347	0.84[ASN][1000 genomes]
rs12343169	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12380322	0.85[EUR][1000 genomes]
rs13287117	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13287517	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1932457	0.84[ASN][1000 genomes]
rs2130570	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130571	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35133951	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4392990	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4394488	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4439216	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4977278	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4977490	0.81[AMR][1000 genomes]
rs4977492	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62563593	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62563594	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6475311	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6475312	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6475313	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475314	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6475315	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs68092871	0.85[ASN][1000 genomes]
rs7022450	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7022807	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7026281	0.82[EUR][1000 genomes]
rs7027346	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7035738	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7036118	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7036182	0.85[ASN][1000 genomes]
rs7036301	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7037772	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7037787	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7043115	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7043507	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7045844	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7467618	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7850487	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7854974	0.86[ASN][1000 genomes]
rs7855250	0.85[ASN][1000 genomes]
rs7855338	0.83[ASN][1000 genomes]
rs7856768	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9298795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2233798	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048000-19050600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr9:19048200-19049000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr9:19048200-19049000	Flanking Active TSS	Dnd41	blood
4	chr9:19048200-19050400	Active TSS	HSMM	muscle
5	chr9:19048400-19049000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:19048400-19049000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr9:19048400-19049000	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr9:19048400-19049000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:19048400-19049000	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr9:19048400-19049000	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr9:19048400-19049000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr9:19048400-19049000	Flanking Active TSS	Rectal Smooth Muscle	rectum
13	chr9:19048400-19049000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr9:19048400-19049000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr9:19048400-19049000	Flanking Active TSS	NHEK	skin
16	chr9:19048400-19049000	Flanking Active TSS	NHLF	lung
17	chr9:19048400-19049000	Flanking Active TSS	Osteobl	bone
18	chr9:19048400-19049200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr9:19048400-19049200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:19048400-19049200	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr9:19048400-19050000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:19048400-19050200	Active TSS	H1 Cell Line	embryonic stem cell
23	chr9:19048400-19050200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:19048400-19050400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:19048400-19050400	Active TSS	Colon Smooth Muscle	Colon
26	chr9:19048400-19050600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:19048400-19050600	Active TSS	Brain Anterior Caudate	brain
28	chr9:19048400-19050600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:19048400-19050800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:19048400-19050800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:19048400-19050800	Active TSS	A549	lung
32	chr9:19048400-19051000	Active TSS	Fetal Kidney	kidney
33	chr9:19048400-19051000	Active TSS	K562	blood
34	chr9:19048400-19051000	Active TSS	NHDF-Ad	bronchial
35	chr9:19048400-19051200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr9:19048400-19051200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr9:19048400-19051200	Active TSS	Colonic Mucosa	Colon
38	chr9:19048400-19051200	Active TSS	Right Ventricle	heart
39	chr9:19048400-19051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr9:19048400-19051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr9:19048400-19051600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr9:19048400-19051800	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr9:19048400-19051800	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr9:19048600-19049000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr9:19048600-19049000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:19048600-19049000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr9:19048600-19049000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:19048600-19049000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr9:19048600-19049000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:19048600-19049000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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