Variant report

Variant	rs538180033
Chromosome Location	chr1:9750377-9750378
allele	A/G
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	chr1:9750240-9750390	HA-sp	spinal cord:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
2	CTCF	chr1:9750300-9750450	AG10803	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
3	MAX	chr1:9749952-9750459	A549	lung:	n/a	n/a
4	JUND	chr1:9750106-9750474	K562	blood:	n/a	n/a
5	CTCF	chr1:9750260-9750410	HMEC	breast:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
6	CTCFL	chr1:9750238-9750415	K562	blood:	n/a	n/a
7	SIN3A	chr1:9748978-9750817	H1-hESC	embryonic stem cell:	n/a	chr1:9750298-9750311 chr1:9750560-9750574
8	CTCF	chr1:9750240-9750390	HCFaa	heart:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
9	RAD21	chr1:9750096-9750457	IMR90	lung:	n/a	chr1:9750318-9750337 chr1:9750324-9750333
10	MAX	chr1:9749876-9750514	ECC-1	luminal epithelium:	n/a	chr1:9749944-9749954
11	CTCF	chr1:9750280-9750430	AoAF	blood vessel:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
12	CTCF	chr1:9750300-9750450	HAc	cerebellar:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
13	CHD2	chr1:9750018-9750511	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr1:9750179-9750405	T-47D	breast:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
15	CTCF	chr1:9750253-9750382	NHEK	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
16	CTCF	chr1:9750260-9750410	HepG2	liver:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
17	FOXA2	chr1:9749832-9750452	A549	lung:	n/a	n/a
18	CTCF	chr1:9750280-9750430	HPAF	blood vessel:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
19	ZBTB7A	chr1:9748993-9750468	ECC-1	luminal epithelium:	n/a	chr1:9749244-9749253
20	POLR2A	chr1:9749122-9750384	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXA2	chr1:9749995-9750400	A549	lung:	n/a	n/a
22	CTCF	chr1:9750240-9750390	Caco-2	colon:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
23	CTCF	chr1:9750320-9750470	HCM	heart:	n/a	chr1:9750321-9750337 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
24	CTCF	chr1:9750240-9750390	NHDF-neo	bronchial:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
25	CTCF	chr1:9750249-9750408	HepG2	liver:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
26	CTCF	chr1:9750297-9750381	Pancreas_OC	pancreas:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
27	TBL1XR1	chr1:9750236-9750382	K562	blood:	n/a	n/a
28	CTCF	chr1:9750280-9750430	A549	lung:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
29	CTCF	chr1:9750260-9750410	BJ	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
30	MXI1	chr1:9749957-9751852	IMR90	lung:	n/a	n/a
31	CTCF	chr1:9750260-9750410	HPF	lung:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
32	CTCF	chr1:9750240-9750390	WERI-Rb-1	eye:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
33	CTCF	chr1:9750286-9750398	HUVEC	blood vessel:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
34	MAX	chr1:9749823-9750419	K562	blood:	n/a	chr1:9749944-9749954
35	CTCF	chr1:9750260-9750410	RPTEC	kidney:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
36	CTCF	chr1:9750260-9750410	HCM	heart:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
37	WRNIP1	chr1:9750139-9750465	GM12878	blood:	n/a	n/a
38	CTCF	chr1:9750240-9750390	AG04450	lung:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
39	CTCF	chr1:9750300-9750450	HMEC	breast:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
40	CTCF	chr1:9750260-9750410	AG09319	gingival:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
41	CTCF	chr1:9750276-9750377	K562	blood:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
42	CTCF	chr1:9750240-9750390	BJ	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
43	MAX	chr1:9749947-9750555	A549	lung:	n/a	n/a
44	CTCF	chr1:9750260-9750410	HCPEpiC	choroid plexus:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
45	CTCF	chr1:9750148-9750439	A549	lung:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
46	CTCF	chr1:9750260-9750410	AG04449	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
47	CTCF	chr1:9750168-9750475	A549	lung:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
48	E2F6	chr1:9749944-9750447	A549	lung:	n/a	n/a
49	CTCF	chr1:9750260-9750410	AG09309	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338
50	CTCF	chr1:9750300-9750450	NHEK	skin:	n/a	chr1:9750321-9750337 chr1:9750315-9750336 chr1:9750322-9750335 chr1:9750322-9750335 chr1:9750320-9750338

No.	Distal block	Cell Line	Cell type
1	chr1:9749593..9751802-chr1:9777886..9780307,2	K562	blood:
2	chr1:9746126..9748956-chr1:9749457..9751271,2	MCF-7	breast:
3	chr1:9745914..9747829-chr1:9748443..9751067,2	K562	blood:
4	chr1:9750156..9751724-chr7:23568721..23571687,2	K562	blood:
5	chr1:9749103..9751299-chr1:9843003..9845112,2	K562	blood:
6	chr1:9748418..9751556-chr1:9755069..9757789,4	K562	blood:
7	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
8	chr1:9686883..9687545-chr1:9749890..9750740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231789	TF binding region
ENSG00000171608	Chromatin interaction
ENSG00000231789	Chromatin interaction
ENSG00000164548	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	esv3408612	chr1:9748390-9751238	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3426414	chr1:9748415-9751113	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3424708	chr1:9748735-9771466	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3338032	chr1:9749165-9750613	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9746800-9750600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:9747000-9750400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:9747000-9750400	Active TSS	HSMM	muscle
4	chr1:9747000-9751200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:9747200-9750400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:9747200-9750400	Active TSS	Aorta	Aorta
7	chr1:9747200-9750600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:9747800-9750400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:9748600-9750600	Active TSS	Right Atrium	heart
10	chr1:9748600-9750600	Active TSS	NHLF	lung
11	chr1:9748800-9750400	Active TSS	HSMMtube	muscle
12	chr1:9748800-9750600	Active TSS	Rectal Smooth Muscle	rectum
13	chr1:9749000-9750400	Active TSS	Lung	lung
14	chr1:9749000-9750400	Active TSS	A549	lung
15	chr1:9749000-9750800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:9749000-9751600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:9749200-9750400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:9749200-9750400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:9749200-9750400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:9749200-9750400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:9749200-9750400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:9749200-9750600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:9749200-9750600	Enhancers	Fetal Heart	heart
24	chr1:9749200-9750800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:9749200-9751000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:9749200-9751000	Active TSS	Fetal Brain Female	brain
27	chr1:9749400-9750400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:9749400-9750400	Enhancers	Liver	Liver
29	chr1:9749400-9750400	Active TSS	Brain Angular Gyrus	brain
30	chr1:9749400-9750400	Active TSS	Brain Anterior Caudate	brain
31	chr1:9749400-9750400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:9749400-9750400	Enhancers	Brain Substantia Nigra	brain
33	chr1:9749400-9750400	Active TSS	Esophagus	oesophagus
34	chr1:9749400-9750400	Active TSS	Left Ventricle	heart
35	chr1:9749400-9750400	Active TSS	Pancreas	Pancrea
36	chr1:9749400-9750600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:9749400-9750800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:9749400-9750800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:9749400-9750800	Enhancers	Spleen	Spleen
40	chr1:9749400-9751000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:9749400-9751600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:9749800-9750400	Enhancers	Dnd41	blood
43	chr1:9750000-9750400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:9750000-9750400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:9750000-9750400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr1:9750000-9750400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
47	chr1:9750000-9750400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr1:9750000-9750400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
49	chr1:9750000-9750400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr1:9750000-9750400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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