Variant report

Variant	rs17137001
Chromosome Location	chr7:7777975-7777976
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	TCF7L2	chr7:7777914-7778230	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7777111..7778841-chr7:7780789..7783193,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270314	TF binding region
ENSG00000269721	Chromatin interaction
ENSG00000234718	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11984316	0.85[CEU][hapmap]
rs1541550	0.84[EUR][1000 genomes]
rs17136857	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17136904	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136971	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17137046	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17137076	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17137195	0.84[EUR][1000 genomes]
rs17137236	0.84[EUR][1000 genomes]
rs2068638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956000	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956186	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958003	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958461	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971274	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979614	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972648	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs17137001	ICA1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7737600-7778800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:7752600-7790400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:7759000-7785800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr7:7759400-7791200	Weak transcription	Esophagus	oesophagus
5	chr7:7759600-7779000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr7:7759600-7780000	Weak transcription	Primary T cells from cord blood	blood
7	chr7:7759600-7786800	Weak transcription	Aorta	Aorta
8	chr7:7760800-7778400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr7:7760800-7785200	Weak transcription	Primary B cells from cord blood	blood
10	chr7:7771000-7785600	Weak transcription	Pancreas	Pancrea
11	chr7:7771200-7785800	Weak transcription	Fetal Intestine Small	intestine
12	chr7:7771600-7783000	Weak transcription	Ovary	ovary
13	chr7:7771600-7784800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:7771600-7785400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:7771600-7791000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:7772000-7786000	Weak transcription	Brain Germinal Matrix	brain
17	chr7:7772200-7784800	Weak transcription	Fetal Heart	heart
18	chr7:7772800-7778600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:7773000-7778800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:7773000-7802000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:7773200-7778200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:7773200-7778200	Weak transcription	Brain Substantia Nigra	brain
23	chr7:7773800-7778200	Weak transcription	HSMM	muscle
24	chr7:7773800-7778400	Weak transcription	HepG2	liver
25	chr7:7774400-7779000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:7775400-7778200	Weak transcription	GM12878-XiMat	blood
27	chr7:7776600-7778200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:7776600-7778200	Weak transcription	Dnd41	blood
29	chr7:7776600-7778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:7776800-7778200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:7776800-7778200	Weak transcription	Fetal Thymus	thymus
32	chr7:7776800-7778400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:7776800-7779400	Weak transcription	HSMMtube	muscle
34	chr7:7776800-7782800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr7:7777000-7778200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:7777000-7778200	Weak transcription	Fetal Muscle Leg	muscle
37	chr7:7777000-7778200	Weak transcription	Psoas Muscle	Psoas
38	chr7:7777000-7778400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:7777200-7778400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:7777200-7778400	Enhancers	Stomach Mucosa	stomach
41	chr7:7777200-7778600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:7777200-7778800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:7777200-7778800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:7777200-7782600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:7777400-7778600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:7777400-7778600	Enhancers	Colon Smooth Muscle	Colon
47	chr7:7777400-7781600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr7:7777600-7778000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:7777800-7778000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:7777800-7779800	Enhancers	Thymus	Thymus

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