Variant report

Variant	rs9401101
Chromosome Location	chr6:119255491-119255492
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	MAX	chr6:119255389-119256540	ECC-1	luminal epithelium:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
2	POLR2A	chr6:119255359-119256710	PFSK-1	brain:	n/a	n/a
3	MAZ	chr6:119255108-119256825	IMR90	lung:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
4	E2F4	chr6:119255452-119256533	MCF10A-Er-Src	breast:	n/a	chr6:119255764-119255775 chr6:119255765-119255774 chr6:119255766-119255773 chr6:119255754-119255763 chr6:119255766-119255773 chr6:119255755-119255769 chr6:119255797-119255807 chr6:119255765-119255773 chr6:119255766-119255773
5	POLR2A	chr6:119255437-119256579	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr6:119255486-119256634	K562	blood:	n/a	n/a
7	TEAD4	chr6:119255432-119256697	K562	blood:	n/a	n/a
8	SIN3AK20	chr6:119255468-119256686	MCF-7	breast:	n/a	n/a
9	POLR2A	chr6:119255452-119256707	GM18505	blood:	n/a	n/a
10	POLR2A	chr6:119255394-119256658	K562	blood:	n/a	n/a
11	EGR1	chr6:119255469-119256617	HCT-116	colon:	n/a	chr6:119255749-119255762 chr6:119255749-119255762 chr6:119255725-119255739
12	MAZ	chr6:119255415-119256719	GM12878	blood:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
13	RCOR1	chr6:119255414-119256662	Hela-S3	cervix:	n/a	n/a
14	RELA	chr6:119255429-119256596	GM15510	blood:	n/a	n/a
15	STAT3	chr6:119255231-119255575	MCF10A-Er-Src	breast:	n/a	chr6:119255251-119255259
16	POLR2A	chr6:119255447-119256660	GM19099	blood:	n/a	n/a
17	MAX	chr6:119255384-119256553	ECC-1	luminal epithelium:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
18	STAT3	chr6:119255416-119255644	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr6:119255382-119256636	NB4	blood:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
20	POLR2A	chr6:119255451-119256652	Raji	blood:	n/a	n/a
21	POLR2A	chr6:119255425-119256627	GM12892	blood:	n/a	n/a
22	POLR2A	chr6:119255292-119256608	Hela-S3	cervix:	n/a	n/a
23	CUX1	chr6:119255302-119255592	GM12878	blood:	n/a	chr6:119255380-119255396
24	POLR2A	chr6:119255462-119256635	GM18951	blood:	n/a	n/a
25	MXI1	chr6:119255355-119256679	IMR90	lung:	n/a	n/a
26	RUNX3	chr6:119255477-119256646	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:119255463-119256652	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:119255235-119256683	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr6:119255381-119256617	MCF-7	breast:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
30	POLR2A	chr6:119255450-119256586	K562	blood:	n/a	n/a
31	SIN3A	chr6:119255471-119256243	GM12878	blood:	n/a	n/a
32	HA-E2F1	chr6:119255345-119256700	MCF-7	breast:	n/a	chr6:119255765-119255774 chr6:119255766-119255773 chr6:119255754-119255763 chr6:119255766-119255773 chr6:119255755-119255769 chr6:119255797-119255807 chr6:119255766-119255773
33	MAX	chr6:119255458-119256492	Hela-S3	cervix:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
34	EGR1	chr6:119255484-119256367	K562	blood:	n/a	chr6:119255749-119255762 chr6:119255749-119255762 chr6:119255725-119255739
35	CREB1	chr6:119255445-119256645	HepG2	liver:	n/a	n/a
36	POLR2A	chr6:119255468-119256673	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr6:119255468-119256689	K562	blood:	n/a	n/a
38	ZNF143	chr6:119255414-119256587	GM12878	blood:	n/a	chr6:119256201-119256219 chr6:119256296-119256314 chr6:119256301-119256311
39	BHLHE40	chr6:119255367-119256535	HepG2	liver:	n/a	n/a
40	HEY1	chr6:119255438-119256687	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:119255419-119256628	MCF-7	breast:	n/a	n/a
42	TBP	chr6:119255318-119255533	GM12878	blood:	n/a	n/a
43	MAX	chr6:119255422-119256665	HepG2	liver:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
44	MAX	chr6:119255441-119256534	GM12878	blood:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
45	POLR2A	chr6:119255367-119256658	GM12878	blood:	n/a	n/a
46	MAX	chr6:119255408-119256571	HepG2	liver:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
47	POLR2A	chr6:119255267-119256667	HepG2	liver:	n/a	n/a
48	MAX	chr6:119255343-119256642	HCT-116	colon:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
49	POLR2A	chr6:119255314-119256662	GM12878	blood:	n/a	n/a
50	E2F6	chr6:119255426-119256520	H1-hESC	embryonic stem cell:	n/a	chr6:119255765-119255774 chr6:119255766-119255773 chr6:119255754-119255763 chr6:119255766-119255773 chr6:119255755-119255769 chr6:119255797-119255807 chr6:119255765-119255773 chr6:119255766-119255773

No.	Distal block	Cell Line	Cell type
1	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
2	chr6:119253156..119256806-chr6:119394976..119399977,7	K562	blood:
3	chr6:119213036..119217484-chr6:119254311..119257675,9	MCF-7	breast:
4	chr6:119242613..119249110-chr6:119251513..119257145,6	MCF-7	breast:
5	chr6:119148024..119150788-chr6:119254470..119256543,2	MCF-7	breast:
6	chr3:155571664..155572210-chr6:119255210..119256056,2	Hela-S3	cervix:
7	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
8	chr6:119253238..119258280-chr6:119398045..119402661,8	K562	blood:
9	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:

Variant related genes	Relation type
ENSG00000253194	TF binding region
ENSG00000111879	Chromatin interaction
ENSG00000169359	Chromatin interaction
ENSG00000111875	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10456918	0.96[EUR][1000 genomes]
rs1068588	0.84[EUR][1000 genomes]
rs11153777	0.90[EUR][1000 genomes]
rs11153778	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs11153780	0.96[EUR][1000 genomes]
rs11153781	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153791	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190099	0.90[EUR][1000 genomes]
rs12202077	0.88[EUR][1000 genomes]
rs12204084	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12204825	0.97[EUR][1000 genomes]
rs12207663	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211725	0.86[EUR][1000 genomes]
rs12213327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213597	0.86[EUR][1000 genomes]
rs17506361	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1775613	1.00[JPT][hapmap]
rs1775617	0.87[EUR][1000 genomes]
rs2295709	0.86[CEU][hapmap]
rs284919	0.82[CEU][hapmap]
rs3756939	1.00[JPT][hapmap]
rs590004	0.84[EUR][1000 genomes]
rs610960	0.84[EUR][1000 genomes]
rs639266	0.83[EUR][1000 genomes]
rs669978	0.84[EUR][1000 genomes]
rs67182660	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6902942	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740819	0.86[EUR][1000 genomes]
rs7750373	0.84[EUR][1000 genomes]
rs7771525	0.87[EUR][1000 genomes]
rs7772912	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7775251	0.86[EUR][1000 genomes]
rs7775275	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs794249	1.00[JPT][hapmap]
rs794614	0.86[CEU][hapmap]
rs813233	0.84[EUR][1000 genomes]
rs9372521	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9374756	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9374760	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374762	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9374770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9374774	0.86[EUR][1000 genomes]
rs9385059	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9387607	1.00[JPT][hapmap]
rs9387618	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9387627	1.00[JPT][hapmap]
rs9387631	0.86[EUR][1000 genomes]
rs9401092	0.95[ASN][1000 genomes]
rs9401094	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9401095	0.95[ASN][1000 genomes]
rs9401096	0.95[ASN][1000 genomes]
rs9401100	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9401110	1.00[ASN][1000 genomes]
rs9401111	1.00[ASN][1000 genomes]
rs9401112	0.81[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	esv16596	chr6:119251007-119272087	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv437523	chr6:119251971-119260280	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9401101	MCM9	cis	parietal	SCAN
rs9401101	BRD7P3	cis	parietal	SCAN
rs9401101	MCM9	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119221200-119255800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:119242800-119255800	Weak transcription	Spleen	Spleen
3	chr6:119245400-119255600	Weak transcription	Pancreas	Pancrea
4	chr6:119245600-119255600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:119252800-119255600	Weak transcription	Small Intestine	intestine
6	chr6:119254000-119257400	Active TSS	GM12878-XiMat	blood
7	chr6:119254400-119255600	Flanking Active TSS	Dnd41	blood
8	chr6:119254600-119255600	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr6:119254600-119257000	Active TSS	Fetal Intestine Large	intestine
10	chr6:119254800-119255600	Flanking Active TSS	Liver	Liver
11	chr6:119254800-119255600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr6:119255000-119255600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:119255000-119255600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:119255000-119255600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:119255000-119255600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:119255000-119255600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr6:119255000-119255600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr6:119255000-119255600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:119255000-119255600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:119255000-119255600	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr6:119255000-119255600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:119255000-119257000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr6:119255000-119257000	Active TSS	HMEC	breast
24	chr6:119255000-119257200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:119255000-119257200	Active TSS	Stomach Smooth Muscle	stomach
26	chr6:119255200-119255600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:119255200-119255600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:119255200-119255600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr6:119255200-119255600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr6:119255200-119255600	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr6:119255200-119255600	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:119255200-119255600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:119255200-119255600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr6:119255200-119255600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:119255200-119255600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:119255200-119255600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:119255200-119255600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:119255200-119255600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:119255200-119255600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:119255200-119255600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:119255200-119255600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr6:119255200-119255600	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr6:119255200-119255600	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr6:119255200-119255600	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr6:119255200-119255600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr6:119255200-119255600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr6:119255200-119255600	Flanking Active TSS	Fetal Brain Male	brain
48	chr6:119255200-119255600	Flanking Active TSS	Fetal Heart	heart
49	chr6:119255200-119255600	Flanking Active TSS	Fetal Kidney	kidney
50	chr6:119255200-119255600	Flanking Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links