Variant report

Variant	rs2068637
Chromosome Location	chr7:7780347-7780348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPA3-2	chr7:7780317-7780751	ENSG00000234718.5

Variant related genes	Relation type
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10486186	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10952069	0.97[ASN][1000 genomes]
rs11760924	0.81[CHB][hapmap]
rs11766846	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154236	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12154244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154665	0.97[ASN][1000 genomes]
rs12154979	0.97[ASN][1000 genomes]
rs12702640	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12702642	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12702643	0.84[ASN][1000 genomes]
rs13222137	0.95[ASN][1000 genomes]
rs13237260	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs13237271	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17136953	0.97[ASN][1000 genomes]
rs17136957	0.97[ASN][1000 genomes]
rs17137036	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024372	0.94[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2024373	0.93[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2110556	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2241075	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34627388	0.97[ASN][1000 genomes]
rs35562533	0.95[ASN][1000 genomes]
rs35844437	0.97[ASN][1000 genomes]
rs36045810	0.97[ASN][1000 genomes]
rs36092641	0.96[ASN][1000 genomes]
rs4725016	0.81[CHB][hapmap]
rs4725019	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725020	0.90[ASN][1000 genomes]
rs4725022	0.94[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6953290	0.81[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6958302	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6972438	0.97[ASN][1000 genomes]
rs717298	0.87[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs73676911	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73676912	0.93[ASN][1000 genomes]
rs7796096	0.97[ASN][1000 genomes]
rs972647	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974989	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974990	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2068637	TNRC18	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr7:7759600-7786800	Weak transcription	Aorta	Aorta
5	chr7:7760800-7785200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:7771000-7785600	Weak transcription	Pancreas	Pancrea
7	chr7:7771200-7785800	Weak transcription	Fetal Intestine Small	intestine
8	chr7:7771600-7783000	Weak transcription	Ovary	ovary
9	chr7:7771600-7784800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:7771600-7785400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:7771600-7791000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:7772000-7786000	Weak transcription	Brain Germinal Matrix	brain
13	chr7:7772200-7784800	Weak transcription	Fetal Heart	heart
14	chr7:7773000-7802000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:7776800-7782800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:7777200-7782600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:7777400-7781600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:7778000-7780400	Enhancers	Rectal Smooth Muscle	rectum
19	chr7:7778200-7780600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr7:7778400-7784800	Weak transcription	Stomach Mucosa	stomach
21	chr7:7778600-7797400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:7779000-7784800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:7779000-7787200	Weak transcription	Small Intestine	intestine
24	chr7:7779600-7786400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:7779800-7782800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:7779800-7785600	Weak transcription	Fetal Thymus	thymus
27	chr7:7779800-7796000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:7779800-7800200	Weak transcription	Thymus	Thymus
29	chr7:7780000-7781800	Weak transcription	Gastric	stomach
30	chr7:7780200-7782600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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