Variant report

Variant	rs10101195
Chromosome Location	chr8:11623212-11623213
allele	A/C
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	CBX3	chr8:11622882-11623304	K562	blood:	n/a	n/a
2	CTCF	chr8:11623059-11623229	A549	lung:	n/a	n/a
3	CTCF	chr8:11622932-11623328	K562	blood:	n/a	n/a
4	MYC	chr8:11622983-11623332	K562	blood:	n/a	chr8:11623155-11623162
5	CTCF	chr8:11623080-11623230	AG10803	skin:	n/a	n/a
6	BRCA1	chr8:11623080-11623288	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr8:11623100-11623250	MCF-7	breast:	n/a	n/a
8	CTCF	chr8:11622845-11623551	HCT-116	colon:	n/a	n/a
9	CTCF	chr8:11622694-11623860	SK-N-SH	brain:	n/a	n/a
10	MAX	chr8:11622940-11623347	K562	blood:	n/a	chr8:11623155-11623162 chr8:11622954-11622963
11	CTCF	chr8:11623100-11623250	HEK293	kidney:	n/a	n/a
12	USF2	chr8:11622956-11623305	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr8:11623080-11623230	NHLF	lung:	n/a	n/a
14	SIN3AK20	chr8:11622954-11623249	SK-N-SH	brain:	n/a	n/a
15	MAX	chr8:11622960-11623384	NB4	blood:	n/a	chr8:11623155-11623162
16	CTCF	chr8:11622965-11623306	Spleen_OC	spleen:	n/a	n/a
17	YY1	chr8:11622975-11623299	GM12878	blood:	n/a	n/a
18	CTCF	chr8:11623100-11623250	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr8:11622976-11623399	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOS	chr8:11623024-11623245	MCF10A-Er-Src	breast:	n/a	n/a
21	CTCF	chr8:11622923-11623347	A549	lung:	n/a	n/a
22	CTCF	chr8:11623100-11623250	AG04450	lung:	n/a	n/a
23	MYC	chr8:11622992-11623332	MCF10A-Er-Src	breast:	n/a	chr8:11623155-11623162
24	CTCF	chr8:11622982-11623295	NHEK	skin:	n/a	n/a
25	FOS	chr8:11622714-11623539	HUVEC	blood vessel:	n/a	chr8:11622953-11622963 chr8:11622954-11622962 chr8:11622952-11622963
26	CTCF	chr8:11623080-11623230	HA-sp	spinal cord:	n/a	n/a
27	CTCF	chr8:11622990-11623296	Gliobla	brain:	n/a	n/a
28	CTCF	chr8:11623100-11623250	AG10803	skin:	n/a	n/a
29	CTCF	chr8:11623080-11623230	HepG2	liver:	n/a	n/a
30	MAX	chr8:11622997-11623337	HepG2	liver:	n/a	chr8:11623155-11623162
31	CTCF	chr8:11623080-11623230	HPAF	blood vessel:	n/a	n/a
32	RAD21	chr8:11622937-11623406	GM12878	blood:	n/a	n/a
33	CTCF	chr8:11623080-11623230	GM12867	blood:	n/a	n/a
34	MAX	chr8:11622987-11623310	K562	blood:	n/a	chr8:11623155-11623162
35	CTCF	chr8:11623100-11623250	NB4	blood:	n/a	n/a
36	RUNX3	chr8:11622903-11623288	GM12878	blood:	n/a	n/a
37	RAD21	chr8:11622772-11623561	ECC-1	luminal epithelium:	n/a	n/a
38	JUND	chr8:11622954-11623350	K562	blood:	n/a	chr8:11622954-11622962
39	USF1	chr8:11622993-11623243	HepG2	liver:	n/a	n/a
40	MYC	chr8:11622954-11623223	H1-hESC	embryonic stem cell:	n/a	chr8:11623155-11623162 chr8:11622954-11622963
41	CTCF	chr8:11623080-11623230	HVMF	connective:	n/a	n/a
42	CTCF	chr8:11623100-11623250	WI-38	lung:	n/a	n/a
43	CTCF	chr8:11622938-11623355	T-47D	breast:	n/a	n/a
44	CTCF	chr8:11622998-11623280	MCF-7	breast:	n/a	n/a
45	RAD21	chr8:11622922-11623380	HepG2	liver:	n/a	n/a
46	USF1	chr8:11623018-11623225	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr8:11623100-11623250	HFF	foreskin:	n/a	n/a
48	CTCF	chr8:11623080-11623230	WERI-Rb-1	eye:	n/a	n/a
49	POU2F2	chr8:11622855-11623325	GM12878	blood:	n/a	n/a
50	RCOR1	chr8:11623035-11623301	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:11622903..11623629-chr8:11815893..11817036,5	K562	blood:
2	chr8:11614600..11617057-chr8:11621350..11623693,3	K562	blood:
3	chr8:11622652..11623752-chr8:11800899..11801806,5	MCF-7	breast:
4	chr8:11622902..11623629-chr8:11759456..11760412,3	MCF-7	breast:
5	chr8:11622750..11623420-chr8:11815244..11815854,2	MCF-7	breast:
6	chr8:11613933..11616620-chr8:11622009..11623693,2	K562	blood:
7	chr8:11622669..11623564-chr8:11800869..11801753,3	K562	blood:

Variant related genes	Relation type
NEIL2	TF binding region
ENSG00000136574	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1534862	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs17153776	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17153782	0.89[ASN][1000 genomes]
rs17754589	0.89[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs2740435	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34928882	0.90[ASN][1000 genomes]
rs66510044	0.90[ASN][1000 genomes]
rs67123108	0.83[EUR][1000 genomes]
rs804270	0.89[ASN][1000 genomes]
rs804271	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs8191530	0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs8191604	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs8191649	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs8191663	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs904009	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10101195	NEIL2	Cis_1M	lymphoblastoid	RTeQTL
rs10101195	XKR6	cis	cerebellum	SCAN
rs10101195	NEIL2	cis	lymphoblastoid	seeQTL
rs10101195	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11615800-11626800	Weak transcription	Left Ventricle	heart
2	chr8:11617000-11626800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:11617400-11626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:11617400-11626400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:11617400-11626800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:11618000-11626000	Weak transcription	Pancreas	Pancrea
7	chr8:11618000-11626800	Weak transcription	Fetal Intestine Large	intestine
8	chr8:11619600-11626800	Weak transcription	Gastric	stomach
9	chr8:11620400-11626600	Weak transcription	Right Ventricle	heart
10	chr8:11621200-11626600	Weak transcription	Fetal Intestine Small	intestine
11	chr8:11621600-11624800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr8:11622000-11623800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:11622000-11623800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:11622000-11623800	Enhancers	HSMM	muscle
15	chr8:11622400-11626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr8:11622600-11623800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:11622600-11623800	Enhancers	NHEK	skin
18	chr8:11622800-11623400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr8:11622800-11623400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:11622800-11623400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr8:11622800-11623400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:11622800-11623400	Enhancers	Brain Anterior Caudate	brain
23	chr8:11622800-11623400	Enhancers	Brain Substantia Nigra	brain
24	chr8:11622800-11623400	Enhancers	Fetal Thymus	thymus
25	chr8:11622800-11623400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr8:11622800-11623600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr8:11622800-11623600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr8:11622800-11623600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr8:11622800-11623600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr8:11622800-11623600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr8:11622800-11623600	Enhancers	Ovary	ovary
32	chr8:11622800-11623600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr8:11622800-11623600	Enhancers	Stomach Mucosa	stomach
34	chr8:11622800-11623800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr8:11622800-11623800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:11622800-11623800	Enhancers	Fetal Heart	heart
37	chr8:11622800-11623800	Enhancers	HSMMtube	muscle
38	chr8:11622800-11624000	Enhancers	Primary B cells from peripheral blood	blood
39	chr8:11622800-11624000	Enhancers	HUVEC	blood vessel
40	chr8:11623000-11623400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr8:11623000-11623400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr8:11623000-11623400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr8:11623000-11623400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr8:11623000-11623400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr8:11623000-11623400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr8:11623000-11623400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr8:11623000-11623400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr8:11623000-11623400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr8:11623000-11623400	Enhancers	Duodenum Mucosa	Duodenum
50	chr8:11623000-11623400	Enhancers	Rectal Smooth Muscle	rectum

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