Variant report

Variant	rs4404880
Chromosome Location	chr8:38823999-38824000
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	RAD21	chr8:38823844-38824467	HCT-116	colon:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
2	RAD21	chr8:38823931-38824391	IMR90	lung:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
3	RAD21	chr8:38823829-38824270	HepG2	liver:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
4	SMC3	chr8:38823933-38824360	GM12878	blood:	n/a	chr8:38824165-38824179
5	SIN3A	chr8:38823971-38824244	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr8:38823887-38824404	MCF-7	breast:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
7	MAZ	chr8:38823957-38824257	K562	blood:	n/a	n/a
8	RUNX3	chr8:38823934-38824239	GM12878	blood:	n/a	n/a
9	MAX	chr8:38823817-38824276	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr8:38823929-38824393	GM12878	blood:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
11	CTCF	chr8:38823980-38824130	GM12867	blood:	n/a	n/a
12	RAD21	chr8:38823888-38824390	ECC-1	luminal epithelium:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
13	RAD21	chr8:38823799-38824410	H1-hESC	embryonic stem cell:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
14	MYC	chr8:38823995-38824272	K562	blood:	n/a	n/a
15	RAD21	chr8:38823883-38824332	SK-N-SH_RA	brain:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
16	CTCF	chr8:38823975-38824274	GM12892	blood:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
17	HCFC1	chr8:38823861-38824246	K562	blood:	n/a	n/a
18	POLR2A	chr8:38823883-38824368	GM12878	blood:	n/a	n/a
19	RAD21	chr8:38823417-38824548	SK-N-SH	brain:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
20	CTCF	chr8:38823911-38824310	HepG2	liver:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
21	CTCF	chr8:38823972-38824278	GM19238	blood:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
22	CTCF	chr8:38823966-38824379	IMR90	lung:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
23	JUND	chr8:38823990-38824273	K562	blood:	n/a	n/a
24	RAD21	chr8:38823888-38824385	Hela-S3	cervix:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
25	MAX	chr8:38823934-38824267	NB4	blood:	n/a	n/a
26	RFX5	chr8:38823934-38824304	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr8:38823924-38824305	K562	blood:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
28	RAD21	chr8:38823983-38824240	K562	blood:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
29	CTCF	chr8:38823903-38824273	GM19240	blood:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
30	RAD21	chr8:38823905-38824454	MCF-7	breast:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
31	CTCF	chr8:38823890-38824284	T-47D	breast:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
32	CTCF	chr8:38823388-38824560	SK-N-SH	brain:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
33	RAD21	chr8:38823923-38824479	A549	lung:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
34	RAD21	chr8:38823934-38824367	HepG2	liver:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
35	RAD21	chr8:38823761-38824459	A549	lung:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
36	CTCF	chr8:38823916-38824366	A549	lung:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
37	RAD21	chr8:38823877-38824407	HepG2	liver:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
38	CTCF	chr8:38823861-38824487	HCT-116	colon:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
39	CTCF	chr8:38823940-38824378	GM12878	blood:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
40	USF2	chr8:38823908-38824087	Hela-S3	cervix:	n/a	n/a
41	RAD21	chr8:38823962-38824343	GM12878	blood:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
42	CTCF	chr8:38823767-38824469	A549	lung:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
43	RAD21	chr8:38823972-38824264	K562	blood:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
44	RAD21	chr8:38823992-38824354	K562	blood:	n/a	chr8:38824161-38824180 chr8:38824164-38824177
45	CTCF	chr8:38823946-38824369	K562	blood:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
46	YY1	chr8:38823913-38824276	GM12878	blood:	n/a	n/a
47	YY1	chr8:38823959-38824261	GM12892	blood:	n/a	n/a
48	CTCF	chr8:38823919-38824299	H1-hESC	embryonic stem cell:	n/a	chr8:38824163-38824181 chr8:38824165-38824178 chr8:38824158-38824179
49	MYC	chr8:38823995-38824337	K562	blood:	n/a	n/a
50	SMC3	chr8:38823870-38824474	SK-N-SH	brain:	n/a	chr8:38824165-38824179

No.	Distal block	Cell Line	Cell type
1	chr8:38707845..38711256-chr8:38821077..38824253,4	MCF-7	breast:
2	chr8:38713358..38714137-chr8:38823718..38824690,5	K562	blood:
3	chr8:38814756..38818427-chr8:38822560..38824207,3	K562	blood:
4	chr8:38687902..38688860-chr8:38823699..38824685,8	K562	blood:
5	chr8:38817416..38820372-chr8:38822881..38825576,2	K562	blood:
6	chr8:38713423..38714279-chr8:38823384..38824403,4	MCF-7	breast:
7	chr8:38688150..38688908-chr8:38823571..38824622,6	MCF-7	breast:
8	chr8:38794301..38797045-chr8:38822308..38824981,2	MCF-7	breast:
9	chr8:38822262..38824083-chr8:38854161..38856355,2	MCF-7	breast:

Variant related genes	Relation type
PLEKHA2	TF binding region
ENSG00000168615	Chromatin interaction
ENSG00000169490	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10958812	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28641150	0.82[AMR][1000 genomes]
rs4301415	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4733893	0.91[EUR][1000 genomes]
rs4733894	0.82[AMR][1000 genomes]
rs4733897	0.81[AMR][1000 genomes]
rs4733958	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4733959	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6474516	0.81[AMR][1000 genomes]
rs6981759	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6985572	0.88[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6996274	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6998440	0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs7007639	0.89[YRI][hapmap];0.95[AFR][1000 genomes]
rs7010131	0.82[AFR][1000 genomes]
rs7295	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9692838	0.87[EUR][1000 genomes]
rs9987126	0.88[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4404880	TM2D2	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38795800-38830600	Weak transcription	Fetal Kidney	kidney
2	chr8:38797000-38831200	Weak transcription	Psoas Muscle	Psoas
3	chr8:38802800-38831000	Weak transcription	K562	blood
4	chr8:38810200-38831000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:38814000-38826000	Weak transcription	Pancreas	Pancrea
6	chr8:38815800-38827200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:38816000-38825600	Weak transcription	HSMMtube	muscle
8	chr8:38816200-38829600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr8:38816200-38830800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr8:38816600-38825200	Genic enhancers	Primary B cells from cord blood	blood
11	chr8:38816800-38831400	Weak transcription	Gastric	stomach
12	chr8:38817000-38826800	Weak transcription	Esophagus	oesophagus
13	chr8:38817400-38827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:38817600-38826800	Weak transcription	Brain Anterior Caudate	brain
15	chr8:38817600-38826800	Weak transcription	Small Intestine	intestine
16	chr8:38817600-38827400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr8:38817600-38831600	Weak transcription	NHEK	skin
18	chr8:38817800-38825400	Weak transcription	Liver	Liver
19	chr8:38817800-38835200	Weak transcription	HepG2	liver
20	chr8:38818000-38825200	Weak transcription	Fetal Intestine Large	intestine
21	chr8:38818200-38824800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr8:38819400-38826000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:38819400-38831200	Weak transcription	NH-A	brain
24	chr8:38819800-38824200	Enhancers	Fetal Thymus	thymus
25	chr8:38819800-38824200	Enhancers	Thymus	Thymus
26	chr8:38819800-38825800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:38819800-38826200	Weak transcription	Aorta	Aorta
28	chr8:38820000-38824200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr8:38820000-38825800	Weak transcription	Fetal Stomach	stomach
30	chr8:38820000-38826000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:38820000-38826200	Weak transcription	HMEC	breast
32	chr8:38820200-38824000	Enhancers	Primary T cells from cord blood	blood
33	chr8:38820200-38825600	Weak transcription	Fetal Lung	lung
34	chr8:38820200-38825800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:38820400-38824200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr8:38820400-38825800	Weak transcription	Ovary	ovary
37	chr8:38820400-38826000	Weak transcription	Adipose Nuclei	Adipose
38	chr8:38820400-38827000	Weak transcription	NHDF-Ad	bronchial
39	chr8:38820600-38825600	Weak transcription	HSMM	muscle
40	chr8:38820600-38825800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr8:38820600-38826000	Weak transcription	Spleen	Spleen
42	chr8:38820600-38826800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr8:38820600-38827000	Weak transcription	Lung	lung
44	chr8:38820800-38825600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:38820800-38826000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr8:38821400-38824200	Genic enhancers	GM12878-XiMat	blood
47	chr8:38821800-38824200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:38821800-38824400	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr8:38822000-38824200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr8:38822000-38824200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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