Variant report

Variant	rs13237260
Chromosome Location	chr7:7779091-7779092
allele	G/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	EP300	chr7:7778813-7779277	GM12878	blood:	n/a	n/a
2	IKZF1	chr7:7779042-7779235	GM12878	blood:	n/a	n/a
3	MEF2A	chr7:7778841-7779339	GM12878	blood:	n/a	chr7:7779151-7779166 chr7:7779176-7779197 chr7:7778953-7778974 chr7:7779181-7779195 chr7:7779176-7779197
4	EP300	chr7:7778754-7779623	GM12878	blood:	n/a	n/a
5	RCOR1	chr7:7778581-7779271	GM12878	blood:	n/a	n/a
6	TCF7L2	chr7:7778778-7779135	HepG2	liver:	n/a	n/a
7	MXI1	chr7:7778904-7779762	GM12878	blood:	n/a	n/a
8	EP300	chr7:7778798-7779306	GM12878	blood:	n/a	n/a
9	NFIC	chr7:7778819-7779435	GM12878	blood:	n/a	n/a
10	FOXA1	chr7:7778945-7779351	HepG2	liver:	n/a	n/a
11	BHLHE40	chr7:7778842-7779627	GM12878	blood:	n/a	n/a
12	NR2F2	chr7:7778833-7779496	HepG2	liver:	n/a	n/a
13	RUNX3	chr7:7778747-7779410	GM12878	blood:	n/a	n/a
14	EP300	chr7:7778926-7779316	HepG2	liver:	n/a	n/a
15	FOXA1	chr7:7778940-7779239	HepG2	liver:	n/a	n/a
16	FOXA1	chr7:7778890-7779331	HepG2	liver:	n/a	n/a
17	CUX1	chr7:7778723-7779439	GM12878	blood:	n/a	n/a
18	MEF2C	chr7:7778872-7779427	GM12878	blood:	n/a	chr7:7779151-7779166 chr7:7779176-7779197 chr7:7779179-7779194 chr7:7778953-7778974 chr7:7779181-7779195 chr7:7779360-7779375 chr7:7779176-7779197
19	EBF1	chr7:7778808-7779214	GM12878	blood:	n/a	n/a
20	CHD2	chr7:7778844-7779662	GM12878	blood:	n/a	n/a
21	RUNX3	chr7:7778926-7779246	GM12878	blood:	n/a	n/a
22	ZNF143	chr7:7778929-7779100	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr7:7778827-7779419	GM12878	blood:	n/a	n/a
24	MEF2A	chr7:7778898-7779420	GM12878	blood:	n/a	chr7:7779151-7779166 chr7:7779176-7779197 chr7:7778953-7778974 chr7:7779181-7779195 chr7:7779360-7779375 chr7:7779176-7779197
25	NFIC	chr7:7778932-7779466	HepG2	liver:	n/a	n/a
26	NR2F2	chr7:7778863-7779427	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7775020..7777800-chr7:7778182..7779689,2	K562	blood:
2	chr7:7756124..7759013-chr7:7778482..7780690,2	K562	blood:

Variant related genes	Relation type
ENSG00000270314	TF binding region
ENSG00000270314	Chromatin interaction
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10486186	0.97[ASN][1000 genomes]
rs10952069	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760924	0.81[CHB][hapmap]
rs11766846	0.97[ASN][1000 genomes]
rs11978169	0.82[EUR][1000 genomes]
rs12154236	0.83[ASN][1000 genomes]
rs12154244	0.97[ASN][1000 genomes]
rs12154665	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154979	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702640	0.95[ASN][1000 genomes]
rs12702642	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12702643	0.83[ASN][1000 genomes]
rs13222137	0.98[ASN][1000 genomes]
rs13237271	0.96[ASN][1000 genomes]
rs17136953	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136957	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17137036	0.97[ASN][1000 genomes]
rs2024372	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2024373	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2068637	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs2110556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2241075	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs34627388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35562533	0.98[ASN][1000 genomes]
rs35844437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36045810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36092641	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4720751	0.81[EUR][1000 genomes]
rs4725016	0.81[CHB][hapmap]
rs4725019	0.97[ASN][1000 genomes]
rs4725020	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4725022	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6953290	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6958302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6972438	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717298	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs73676911	0.94[ASN][1000 genomes]
rs73676912	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7787930	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7796096	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972647	0.94[ASN][1000 genomes]
rs974989	0.90[ASN][1000 genomes]
rs974990	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887482	chr7:7682439-7785047	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv887486	chr7:7712498-7785047	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv1026564	chr7:7734846-7897847	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv887487	chr7:7740914-7802561	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv887488	chr7:7770203-7794484	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv887489	chr7:7770203-7913311	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv818476	chr7:7774684-7779324	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13237260	LOC389458	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7752600-7790400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:7759000-7785800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr7:7759400-7791200	Weak transcription	Esophagus	oesophagus
4	chr7:7759600-7780000	Weak transcription	Primary T cells from cord blood	blood
5	chr7:7759600-7786800	Weak transcription	Aorta	Aorta
6	chr7:7760800-7785200	Weak transcription	Primary B cells from cord blood	blood
7	chr7:7771000-7785600	Weak transcription	Pancreas	Pancrea
8	chr7:7771200-7785800	Weak transcription	Fetal Intestine Small	intestine
9	chr7:7771600-7783000	Weak transcription	Ovary	ovary
10	chr7:7771600-7784800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:7771600-7785400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:7771600-7791000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:7772000-7786000	Weak transcription	Brain Germinal Matrix	brain
14	chr7:7772200-7784800	Weak transcription	Fetal Heart	heart
15	chr7:7773000-7802000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:7776800-7779400	Weak transcription	HSMMtube	muscle
17	chr7:7776800-7782800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:7777200-7782600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:7777400-7781600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:7777800-7779800	Enhancers	Thymus	Thymus
21	chr7:7778000-7780200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:7778000-7780400	Enhancers	Rectal Smooth Muscle	rectum
23	chr7:7778200-7779200	Enhancers	Dnd41	blood
24	chr7:7778200-7779400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr7:7778200-7779800	Enhancers	Fetal Thymus	thymus
26	chr7:7778200-7779800	Enhancers	GM12878-XiMat	blood
27	chr7:7778200-7780000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:7778200-7780600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr7:7778400-7779800	Enhancers	HepG2	liver
30	chr7:7778400-7780000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:7778400-7784800	Weak transcription	Stomach Mucosa	stomach
32	chr7:7778600-7779400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:7778600-7779600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:7778600-7779800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:7778600-7780200	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr7:7778600-7797400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:7778800-7779200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:7778800-7779200	Enhancers	Brain Anterior Caudate	brain
39	chr7:7778800-7779600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:7778800-7779800	Enhancers	Brain Substantia Nigra	brain
41	chr7:7778800-7780000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:7778800-7780000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr7:7779000-7779200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr7:7779000-7779200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr7:7779000-7780000	Enhancers	Fetal Lung	lung
46	chr7:7779000-7784800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:7779000-7787200	Weak transcription	Small Intestine	intestine

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