Variant report

Variant	rs11177830
Chromosome Location	chr12:41086282-41086283
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	POLR2A	chr12:41086245-41086368	A549	lung:	n/a	n/a
2	TBP	chr12:41086010-41086463	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3AK20	chr12:41086117-41086418	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr12:41085622-41087872	SK-N-SH	brain:	n/a	n/a
5	MAX	chr12:41085837-41086654	A549	lung:	n/a	n/a
6	CHD2	chr12:41085895-41086529	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZBTB7A	chr12:41085910-41087256	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr12:41085690-41087908	A549	lung:	n/a	chr12:41086210-41086220 chr12:41087803-41087810 chr12:41086313-41086320 chr12:41086807-41086814 chr12:41086568-41086578
9	SP2	chr12:41085885-41086401	H1-hESC	embryonic stem cell:	n/a	chr12:41086147-41086170
10	POLR2A	chr12:41086201-41086419	A549	lung:	n/a	n/a
11	SIN3A	chr12:41085645-41087692	H1-hESC	embryonic stem cell:	n/a	chr12:41087530-41087541 chr12:41086689-41086702 chr12:41087087-41087096
12	SP2	chr12:41085900-41086420	H1-hESC	embryonic stem cell:	n/a	chr12:41086147-41086170
13	TAF1	chr12:41086025-41086534	A549	lung:	n/a	n/a
14	PBX3	chr12:41085826-41086424	SK-N-SH	brain:	n/a	chr12:41086149-41086169
15	ZBTB7A	chr12:41085920-41086925	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr12:41086064-41086547	H1-neurons	neurons:	n/a	n/a
17	E2F6	chr12:41086145-41087304	A549	lung:	n/a	chr12:41086685-41086695 chr12:41086529-41086544 chr12:41086772-41086782 chr12:41086530-41086542
18	POLR2A	chr12:41085949-41086469	A549	lung:	n/a	n/a
19	SP1	chr12:41085778-41086358	H1-hESC	embryonic stem cell:	n/a	chr12:41086195-41086204 chr12:41086194-41086203 chr12:41086194-41086203 chr12:41086162-41086183
20	PBX3	chr12:41085927-41086449	A549	lung:	n/a	chr12:41086149-41086169
21	NFYB	chr12:41086004-41086294	K562	blood:	n/a	chr12:41086161-41086175 chr12:41086161-41086176
22	PBX3	chr12:41085856-41086448	SK-N-SH	brain:	n/a	chr12:41086149-41086169
23	POLR2A	chr12:41086039-41086573	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr12:41085923-41086495	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr12:41085689-41087841	A549	lung:	n/a	chr12:41087579-41087589
26	CREB1	chr12:41085950-41086677	A549	lung:	n/a	n/a
27	CTBP2	chr12:41085963-41087461	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr12:41086145-41086479	H1-hESC	embryonic stem cell:	n/a	n/a
29	SP1	chr12:41085785-41087812	A549	lung:	n/a	chr12:41086195-41086204 chr12:41086194-41086203 chr12:41087578-41087590 chr12:41086948-41086957 chr12:41086739-41086753 chr12:41087580-41087589 chr12:41086194-41086203 chr12:41086473-41086482 chr12:41086460-41086474 chr12:41087579-41087588 chr12:41086471-41086483 chr12:41087578-41087590 chr12:41086738-41086747 chr12:41087579-41087589 chr12:41086471-41086483 chr12:41087579-41087589 chr12:41086472-41086481 chr12:41086162-41086183
30	SP1	chr12:41085725-41086638	A549	lung:	n/a	chr12:41086195-41086204 chr12:41086194-41086203 chr12:41086194-41086203 chr12:41086473-41086482 chr12:41086460-41086474 chr12:41086471-41086483 chr12:41086471-41086483 chr12:41086472-41086481 chr12:41086162-41086183
31	SRF	chr12:41086104-41086426	ECC-1	luminal epithelium:	n/a	chr12:41086195-41086205
32	SP1	chr12:41085982-41086319	GM12878	blood:	n/a	chr12:41086195-41086204 chr12:41086194-41086203 chr12:41086194-41086203 chr12:41086162-41086183
33	PBX3	chr12:41085844-41086477	A549	lung:	n/a	chr12:41086149-41086169
34	SP1	chr12:41085879-41086420	H1-hESC	embryonic stem cell:	n/a	chr12:41086195-41086204 chr12:41086194-41086203 chr12:41086194-41086203 chr12:41086162-41086183
35	REST	chr12:41085908-41088056	H1-neurons	neurons:	n/a	chr12:41087530-41087543 chr12:41086366-41086379 chr12:41086362-41086382 chr12:41087533-41087546 chr12:41087479-41087488
36	POLR2A	chr12:41086200-41086390	A549	lung:	n/a	n/a
37	NFYB	chr12:41085987-41086348	GM12878	blood:	n/a	chr12:41086161-41086175 chr12:41086161-41086176

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:41086282-41086332	T-47D	breast:	n/a
2	chr12:41086282-41086332	GM19239	blood:	n/a
3	chr12:41086274-41086324	Jurkat	blood:	n/a
4	chr12:41086282-41086332	MCF-7	breast:	n/a
5	chr12:41086274-41086324	HNPCEpiC	eye:	n/a
6	chr12:41086274-41086324	A549	lung:	n/a
7	chr12:41086282-41086332	SK-N-SH_RA	brain:	n/a
8	chr12:41086274-41086324	PFSK-1	brain:	n/a
9	chr12:41086277-41086327	HCM	heart:	n/a
10	chr12:41086282-41086332	A549	lung:	n/a
11	chr12:41086282-41086332	AG09319	gingival:	n/a
12	chr12:41086282-41086332	GM12891	blood:	n/a
13	chr12:41086277-41086327	NH-A	brain:	n/a
14	chr12:41086282-41086332	Hepatocyte	liver:	n/a
15	chr12:41086274-41086324	ProgFib	skin:	n/a
16	chr12:41086282-41086332	HAEpiC	amniotic membrane:	n/a
17	chr12:41086282-41086332	PrEC	prostate:	n/a
18	chr12:41086274-41086324	AG10803	skin:	n/a
19	chr12:41086282-41086332	HCF	heart:	n/a
20	chr12:41086282-41086332	NHBE	bronchial:	n/a
21	chr12:41086277-41086327	Jurkat	blood:	n/a
22	chr12:41086277-41086327	SK-N-SH_RA	brain:	n/a
23	chr12:41086274-41086324	HRCEpiC	kidney:	n/a
24	chr12:41086274-41086324	LNCaP	prostate:	n/a
25	chr12:41086274-41086324	SK-N-SH	brain:	n/a
26	chr12:41086277-41086327	HUVEC	blood vessel:	n/a
27	chr12:41086274-41086324	Hepatocyte	liver:	n/a
28	chr12:41086277-41086327	PrEC	prostate:	n/a
29	chr12:41086277-41086327	SKMC	muscle:	n/a
30	chr12:41086277-41086327	HEK293	kidney:	embryo
31	chr12:41086274-41086324	HAEpiC	amniotic membrane:	n/a
32	chr12:41086277-41086327	HL-60	blood:	n/a
33	chr12:41086282-41086332	HRCEpiC	kidney:	n/a
34	chr12:41086282-41086332	HUVEC	blood vessel:	n/a
35	chr12:41086274-41086324	AoSMC	blood vessel:	n/a
36	chr12:41086282-41086332	SKMC	muscle:	n/a
37	chr12:41086274-41086324	SKMC	muscle:	n/a
38	chr12:41086274-41086324	HPAEpiC	pulmonary alveolar:	n/a
39	chr12:41086282-41086332	MCF10A-Er-Src	breast:	n/a
40	chr12:41086277-41086327	LNCaP	prostate:	n/a
41	chr12:41086274-41086324	BJ	skin:	n/a
42	chr12:41086274-41086324	HRE	kidney:	n/a
43	chr12:41086274-41086324	U87	brain:	n/a
44	chr12:41086274-41086324	IMR90	lung:	fetal
45	chr12:41086282-41086332	HRPEpiC	eye:	n/a
46	chr12:41086282-41086332	GM06990	blood:	n/a
47	chr12:41086282-41086332	NT2-D1	testis:	n/a
48	chr12:41086277-41086327	K562	blood:	n/a
49	chr12:41086277-41086327	NHBE	bronchial:	n/a
50	chr12:41086277-41086327	PFSK-1	brain:	n/a

Variant related genes	Relation type
CNTN1	TF binding region
CNTN1	CpG island

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17539379	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36131108	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv832378	chr12:40943111-41132305	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2751098	chr12:41082399-41180235	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41085400-41086800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:41085400-41086800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:41085400-41087200	Active TSS	Brain Angular Gyrus	brain
4	chr12:41085600-41086800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr12:41085600-41087000	Active TSS	Fetal Brain Female	brain
6	chr12:41085600-41087600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr12:41085600-41087600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
8	chr12:41085600-41087600	Active TSS	Colon Smooth Muscle	Colon
9	chr12:41085600-41087600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr12:41085600-41087600	Active TSS	NHDF-Ad	bronchial
11	chr12:41085600-41087800	Bivalent/Poised TSS	Fetal Lung	lung
12	chr12:41085600-41088000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:41085600-41088000	Active TSS	Fetal Brain Male	brain
14	chr12:41085600-41088400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:41085800-41086600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:41085800-41086600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:41085800-41086800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:41085800-41086800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:41085800-41087000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr12:41085800-41087000	Active TSS	Ovary	ovary
21	chr12:41085800-41087000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr12:41085800-41087200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr12:41085800-41087200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr12:41085800-41087200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
25	chr12:41085800-41087400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:41085800-41087400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:41085800-41087400	Active TSS	Aorta	Aorta
28	chr12:41085800-41087400	Enhancers	Fetal Heart	heart
29	chr12:41085800-41087400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr12:41085800-41087400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr12:41085800-41087400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
32	chr12:41085800-41087600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr12:41085800-41087600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:41085800-41087600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:41085800-41087600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:41085800-41087600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
37	chr12:41085800-41087800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:41085800-41087800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:41085800-41087800	Active TSS	Fetal Kidney	kidney
40	chr12:41085800-41087800	Active TSS	A549	lung
41	chr12:41085800-41088000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:41085800-41088000	Active TSS	Brain Anterior Caudate	brain
43	chr12:41086000-41086400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:41086000-41086400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
45	chr12:41086000-41086400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:41086000-41086400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr12:41086000-41086600	Active TSS	Psoas Muscle	Psoas
48	chr12:41086000-41086800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
49	chr12:41086000-41086800	Bivalent/Poised TSS	Esophagus	oesophagus
50	chr12:41086000-41087000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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