Variant report

Variant	rs9361235
Chromosome Location	chr6:78175842-78175843
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	CTCF	chr6:78175679-78175948	T-47D	breast:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
2	RAD21	chr6:78175670-78176127	H1-hESC	embryonic stem cell:	n/a	chr6:78175859-78175878
3	CTCF	chr6:78175747-78175989	MCF-7	breast:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
4	CTCF	chr6:78175737-78175947	K562	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
5	CTCF	chr6:78175720-78175870	Caco-2	colon:	n/a	n/a
6	CTCF	chr6:78175726-78176045	GM19238	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
7	CTCF	chr6:78175760-78175910	NHLF	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
8	RAD21	chr6:78175566-78176140	HCT-116	colon:	n/a	chr6:78175859-78175878
9	POLR2A	chr6:78175807-78175966	GM12878	blood:	n/a	n/a
10	CTCF	chr6:78175760-78175910	NHDF-neo	bronchial:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
11	RAD21	chr6:78175596-78176152	H1-hESC	embryonic stem cell:	n/a	chr6:78175859-78175878
12	CTCF	chr6:78175820-78175970	GM12865	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
13	RAD21	chr6:78175602-78176111	A549	lung:	n/a	chr6:78175859-78175878
14	CTCF	chr6:78175780-78175930	AG09319	gingival:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
15	CTCF	chr6:78175820-78175970	HMF	breast:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
16	CTCF	chr6:78175740-78175890	HCT-116	colon:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
17	CTCF	chr6:78175780-78175930	GM06990	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
18	YY1	chr6:78175763-78176481	SK-N-SH	brain:	n/a	chr6:78176265-78176275
19	TCF7L2	chr6:78175633-78176203	PANC-1	pancreas:	n/a	n/a
20	CTCF	chr6:78175780-78175930	HCM	heart:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
21	ZNF143	chr6:78175676-78176730	GM12878	blood:	n/a	chr6:78176069-78176088
22	CTCF	chr6:78175800-78175950	HMEC	breast:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
23	CTCF	chr6:78175820-78175970	NHEK	skin:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
24	STAT3	chr6:78175754-78176107	MCF10A-Er-Src	breast:	n/a	chr6:78175936-78175959 chr6:78175934-78175945
25	RUNX3	chr6:78175650-78176511	GM12878	blood:	n/a	chr6:78176123-78176140
26	RAD21	chr6:78175664-78176846	GM12878	blood:	n/a	chr6:78175859-78175878
27	CTCF	chr6:78175750-78175956	LNCaP	prostate:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
28	CTCF	chr6:78175696-78176058	HepG2	liver:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
29	RAD21	chr6:78175771-78176040	A549	lung:	n/a	chr6:78175859-78175878
30	CTCF	chr6:78175820-78175970	HCT-116	colon:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
31	CTCF	chr6:78175800-78175950	GM12874	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
32	CTCF	chr6:78175800-78175950	AG04449	skin:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
33	CTCF	chr6:78175803-78175957	Lung_OC	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
34	TBL1XR1	chr6:78175492-78176028	GM12878	blood:	n/a	n/a
35	WRNIP1	chr6:78175678-78176705	GM12878	blood:	n/a	n/a
36	CTCF	chr6:78175484-78176132	A549	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
37	CTCF	chr6:78175780-78175930	HEK293	kidney:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
38	CTCF	chr6:78175800-78175950	HPAF	blood vessel:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
39	CTCF	chr6:78175820-78175970	AG04450	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
40	RAD21	chr6:78175601-78176054	A549	lung:	n/a	chr6:78175859-78175878
41	CTCF	chr6:78175800-78175950	SK-N-SH_RA	brain:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
42	CTCF	chr6:78175680-78175977	T-47D	breast:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
43	CTCF	chr6:78175760-78175910	GM12873	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
44	CTCF	chr6:78175757-78176008	A549	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
45	CTCF	chr6:78175800-78175950	HBMEC	blood vessel:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
46	SPI1	chr6:78175814-78176829	GM12878	blood:	n/a	chr6:78176761-78176770 chr6:78176326-78176339
47	POLR2A	chr6:78175688-78176041	HUVEC	blood vessel:	n/a	n/a
48	CUX1	chr6:78175672-78176091	GM12878	blood:	n/a	n/a
49	RAD21	chr6:78175703-78176051	HepG2	liver:	n/a	chr6:78175859-78175878
50	HDAC2	chr6:78175683-78176045	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:78175755..78176369-chr6:78410019..78410778,2	MCF-7	breast:

Variant related genes	Relation type
HTR1B	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11568817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1213356	0.85[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs1213357	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1213366	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1213371	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1213373	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1228814	1.00[CEU][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs130058	0.82[JPT][hapmap]
rs1361847	0.85[CHB][hapmap]
rs17273700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56088227	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361233	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361234	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534282	chr6:77764575-78351994	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1034979	chr6:77781244-78426249	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538324	chr6:77781244-78426249	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1015307	chr6:77902559-78352291	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1028259	chr6:78059491-78709871	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv538325	chr6:78059491-78709871	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2758062	chr6:78100020-78283042	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2759445	chr6:78100020-78283042	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9361235	COL12A1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78174200-78176800	Flanking Active TSS	HUVEC	blood vessel
2	chr6:78174600-78176400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:78175000-78176200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:78175400-78176200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:78175400-78176600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:78175400-78177000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:78175400-78177200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:78175400-78177200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:78175600-78176000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:78175600-78176000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:78175600-78176000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
12	chr6:78175600-78176000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:78175600-78176000	Bivalent/Poised TSS	Left Ventricle	heart
14	chr6:78175600-78176000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:78175600-78176000	Bivalent Enhancer	HepG2	liver
16	chr6:78175600-78176200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
17	chr6:78175600-78176200	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
18	chr6:78175600-78176200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:78175600-78176200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
20	chr6:78175600-78176400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:78175600-78176400	Active TSS	A549	lung
22	chr6:78175600-78176600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
23	chr6:78175600-78176600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
24	chr6:78175600-78176800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:78175600-78176800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:78175600-78176800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr6:78175600-78176800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
28	chr6:78175600-78176800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:78175600-78176800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:78175600-78176800	Active TSS	Aorta	Aorta
31	chr6:78175600-78176800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr6:78175600-78176800	Active TSS	Fetal Heart	heart
33	chr6:78175600-78176800	Bivalent/Poised TSS	Fetal Kidney	kidney
34	chr6:78175600-78176800	Active TSS	Ovary	ovary
35	chr6:78175600-78176800	Active TSS	GM12878-XiMat	blood
36	chr6:78175600-78177000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:78175600-78177000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:78175600-78177000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:78175600-78177000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
40	chr6:78175600-78177000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
41	chr6:78175600-78177000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:78175600-78177000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
43	chr6:78175600-78177000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr6:78175600-78177000	Active TSS	Right Ventricle	heart
45	chr6:78175600-78177200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:78175800-78176000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:78175800-78176000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:78175800-78176000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
49	chr6:78175800-78176000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr6:78175800-78176000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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