Variant report

Variant	rs9461856
Chromosome Location	chr6:33395199-33395200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33394634-33395302	H1-neurons	neurons:	n/a	n/a
2	NR2F2	chr6:33395035-33395678	K562	blood:	n/a	n/a
3	ZBTB7A	chr6:33394801-33396233	K562	blood:	n/a	chr6:33395249-33395263
4	ZBTB7A	chr6:33394843-33396480	ECC-1	luminal epithelium:	n/a	chr6:33395249-33395263
5	MXI1	chr6:33392524-33397784	SK-N-SH	brain:	n/a	chr6:33394814-33394829 chr6:33394812-33394827 chr6:33394872-33394881 chr6:33394456-33394471
6	MAZ	chr6:33395109-33397100	IMR90	lung:	n/a	n/a
7	MAX	chr6:33394868-33395657	NB4	blood:	n/a	n/a
8	ZBTB7A	chr6:33394969-33396487	K562	blood:	n/a	chr6:33395249-33395263
9	POLR2A	chr6:33394784-33396710	Raji	blood:	n/a	n/a
10	POLR2A	chr6:33394812-33395199	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr6:33395195-33396635	K562	blood:	n/a	n/a
12	STAT5A	chr6:33394909-33395702	GM12878	blood:	n/a	n/a
13	ZBTB7A	chr6:33394945-33396431	ECC-1	luminal epithelium:	n/a	chr6:33395249-33395263
14	MXI1	chr6:33394820-33397262	IMR90	lung:	n/a	chr6:33394872-33394881
15	CTCF	chr6:33395120-33395270	HRPEpiC	eye:	n/a	n/a
16	MXI1	chr6:33394816-33395784	GM12878	blood:	n/a	chr6:33394872-33394881
17	POLR2A	chr6:33395156-33396675	K562	blood:	n/a	n/a

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr11:69453730..69455755-chr6:33394973..33397171,2	MCF-7	breast:
3	chr6:33263619..33269524-chr6:33392449..33400505,13	K562	blood:
4	chr6:33283041..33291527-chr6:33390658..33398493,18	K562	blood:
5	chr6:33311665..33314646-chr6:33394060..33395716,2	K562	blood:
6	chr6:32937058..32938880-chr6:33394443..33397147,2	K562	blood:
7	chr6:33392300..33395210-chr6:33647730..33650382,2	MCF-7	breast:
8	chr6:33238574..33240748-chr6:33393246..33395799,2	MCF-7	breast:
9	chr6:32939106..32941739-chr6:33393311..33396155,4	K562	blood:
10	chr6:33376532..33378307-chr6:33395106..33396877,2	MCF-7	breast:
11	chr6:33238168..33246812-chr6:33390354..33398427,26	K562	blood:
12	chr6:33280655..33282668-chr6:33393419..33397905,7	K562	blood:
13	chr6:33215214..33217895-chr6:33392172..33395839,3	K562	blood:
14	chr6:32936581..32938342-chr6:33393160..33395654,2	K562	blood:
15	chr6:33392929..33396981-chr6:33537285..33540754,6	MCF-7	breast:
16	chr6:33392449..33400629-chr6:33419013..33424035,12	MCF-7	breast:
17	chr6:33395175..33398193-chr6:33670762..33673349,3	MCF-7	breast:
18	chr6:33238378..33242418-chr6:33393683..33397768,6	MCF-7	breast:
19	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
20	chr6:33356676..33362230-chr6:33391756..33396223,11	K562	blood:
21	chr6:33254824..33258515-chr6:33394130..33398725,7	K562	blood:
22	chr6:33213767..33216511-chr6:33394618..33396286,2	K562	blood:
23	chr6:33394086..33395846-chr6:33548309..33550543,2	K562	blood:
24	chr6:33171043..33174774-chr6:33394411..33396707,3	K562	blood:
25	chr6:33393221..33396330-chr6:33404523..33406240,3	MCF-7	breast:
26	chr6:33393869..33396201-chr6:33479107..33481448,2	MCF-7	breast:
27	chr6:33392424..33395335-chr6:33538728..33540669,5	K562	blood:
28	chr6:33393532..33395218-chr6:33409993..33412120,3	MCF-7	breast:
29	chr6:33392315..33397649-chr6:33418358..33425832,9	K562	blood:
30	chr6:33265065..33267440-chr6:33393801..33396358,3	MCF-7	breast:
31	chr6:33283215..33284795-chr6:33393304..33395284,2	MCF-7	breast:
32	chr6:32937079..32939347-chr6:33393760..33395327,2	MCF-7	breast:
33	chr6:33394909..33396953-chr6:33473800..33476253,2	MCF-7	breast:
34	chr6:33394932..33398976-chr6:33412593..33416199,4	MCF-7	breast:
35	chr6:33393960..33395826-chr6:33421036..33423799,4	MCF-7	breast:
36	chr6:33171898..33174531-chr6:33393519..33397558,3	K562	blood:
37	chr6:33263595..33269524-chr6:33390524..33397848,10	K562	blood:

No data

Variant related genes	Relation type
SYNGAP1	TF binding region
ENSG00000264085	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000272217	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000236104	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11757273	0.82[ASN][1000 genomes]
rs12204193	0.89[ASN][1000 genomes]
rs1613451	0.85[ASN][1000 genomes]
rs1755045	0.93[ASN][1000 genomes]
rs1755046	0.90[ASN][1000 genomes]
rs1755047	0.85[ASN][1000 genomes]
rs1755048	0.87[ASN][1000 genomes]
rs1755049	0.89[ASN][1000 genomes]
rs2076775	0.89[ASN][1000 genomes]
rs211456	0.88[ASN][1000 genomes]
rs2247385	0.88[ASN][1000 genomes]
rs2274730	0.90[ASN][1000 genomes]
rs2480487	0.84[ASN][1000 genomes]
rs2747477	0.80[ASN][1000 genomes]
rs2747479	0.80[ASN][1000 genomes]
rs2772373	0.87[ASN][1000 genomes]
rs2772375	0.92[ASN][1000 genomes]
rs2772376	0.88[ASN][1000 genomes]
rs2772387	0.84[ASN][1000 genomes]
rs2772389	0.84[ASN][1000 genomes]
rs2772390	0.84[ASN][1000 genomes]
rs2772391	0.91[ASN][1000 genomes]
rs2772392	0.83[ASN][1000 genomes]
rs3117320	0.83[ASN][1000 genomes]
rs3130025	0.84[ASN][1000 genomes]
rs371005	0.83[ASN][1000 genomes]
rs376006	0.86[ASN][1000 genomes]
rs411136	0.85[ASN][1000 genomes]
rs442745	0.90[ASN][1000 genomes]
rs453590	0.88[ASN][1000 genomes]
rs456993	0.86[ASN][1000 genomes]
rs459927	0.82[ASN][1000 genomes]
rs461887	0.85[ASN][1000 genomes]
rs461964	0.80[ASN][1000 genomes]
rs4620113	0.88[ASN][1000 genomes]
rs465223	0.80[ASN][1000 genomes]
rs465474	0.86[ASN][1000 genomes]
rs465506	0.80[ASN][1000 genomes]
rs465877	0.82[ASN][1000 genomes]
rs4711325	0.83[ASN][1000 genomes]
rs4713625	0.91[ASN][1000 genomes]
rs66840884	0.82[ASN][1000 genomes]
rs9357159	0.82[ASN][1000 genomes]
rs9380355	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
6	esv3425065	chr6:33392374-33395872	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
7	esv3329984	chr6:33392649-33396572	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
8	esv3357314	chr6:33393074-33395422	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9461856	TAPBP	cis	Artery Tibial	GTEx
rs9461856	LEMD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33392600-33395600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:33392800-33395600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:33392800-33396200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:33392800-33396600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:33393000-33396400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:33393200-33396000	Active TSS	Right Atrium	heart
7	chr6:33393200-33396200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:33393400-33396200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:33393800-33395600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr6:33393800-33395600	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr6:33393800-33395600	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr6:33393800-33395600	Flanking Active TSS	Fetal Thymus	thymus
13	chr6:33394000-33395200	Enhancers	Placenta	Placenta
14	chr6:33394000-33395200	Weak transcription	Gastric	stomach
15	chr6:33394000-33395600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:33394000-33395600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr6:33394000-33395600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:33394000-33395600	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr6:33394200-33395200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:33394200-33395200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:33394200-33395400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:33394200-33395400	Flanking Active TSS	NHEK	skin
23	chr6:33394200-33395600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr6:33394200-33395600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:33394400-33395200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:33394400-33395200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:33394400-33395200	Weak transcription	Ovary	ovary
28	chr6:33394400-33395400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:33394400-33395400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr6:33394400-33395400	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr6:33394400-33395400	Flanking Active TSS	NHLF	lung
32	chr6:33394400-33395600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr6:33394400-33395600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:33394400-33395600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:33394400-33395600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:33394400-33395600	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr6:33394400-33395600	Flanking Active TSS	Fetal Brain Male	brain
38	chr6:33394400-33395600	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr6:33394400-33395600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr6:33394600-33395200	Enhancers	Fetal Stomach	stomach
41	chr6:33394600-33395200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr6:33394600-33395400	Enhancers	Spleen	Spleen
43	chr6:33394600-33395600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:33394600-33395600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:33394600-33395600	Flanking Active TSS	HMEC	breast
46	chr6:33394600-33395600	Flanking Active TSS	Osteobl	bone
47	chr6:33394800-33395200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
48	chr6:33394800-33395200	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr6:33394800-33395200	Flanking Active TSS	Fetal Kidney	kidney
50	chr6:33394800-33395200	Enhancers	Lung	lung

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