Variant report

Variant	rs6461641
Chromosome Location	chr7:22197748-22197749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10228358	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10242092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10255486	1.00[CEU][hapmap];1.00[CHB][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]
rs10268307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282222	1.00[CHB][hapmap]
rs10950895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763898	1.00[CHB][hapmap]
rs12530484	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12533150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223956	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981598	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079478	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs28411164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28435496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28656168	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4590334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719686	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722104	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722105	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722108	1.00[CHB][hapmap]
rs4722110	1.00[CHB][hapmap]
rs5014150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6461640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][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]
rs6944433	0.93[AFR][1000 genomes]
rs6948973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949461	1.00[CHB][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]
rs6960216	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965394	1.00[CHB][hapmap]
rs6971344	1.00[CEU][hapmap];1.00[CHB][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]
rs6980127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808688	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][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]
rs9886139	1.00[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6461641	SCGB2A2	trans	brain	seeQTL
rs6461641	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:22159800-22214000	Weak transcription	Small Intestine	intestine
2	chr7:22162200-22198000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:22176200-22198200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr7:22176400-22203200	Weak transcription	Stomach Mucosa	stomach
5	chr7:22179600-22206600	Weak transcription	Fetal Stomach	stomach
6	chr7:22181400-22199000	Weak transcription	Gastric	stomach
7	chr7:22184600-22240600	Weak transcription	Colonic Mucosa	Colon
8	chr7:22187000-22204800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:22187200-22199000	Weak transcription	Fetal Brain Male	brain
10	chr7:22190000-22232800	Weak transcription	Aorta	Aorta
11	chr7:22192600-22198200	Genic enhancers	Brain Anterior Caudate	brain
12	chr7:22192600-22199400	Strong transcription	HepG2	liver
13	chr7:22192600-22200800	Strong transcription	Fetal Intestine Large	intestine
14	chr7:22192600-22208200	Strong transcription	Liver	Liver
15	chr7:22192800-22198200	Enhancers	Brain Angular Gyrus	brain
16	chr7:22193600-22207800	Weak transcription	Placenta	Placenta
17	chr7:22193800-22232000	Weak transcription	Adipose Nuclei	Adipose
18	chr7:22194000-22201600	Genic enhancers	Brain Cingulate Gyrus	brain
19	chr7:22194200-22199000	Strong transcription	Fetal Thymus	thymus
20	chr7:22194200-22201200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:22194200-22202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:22194200-22223200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:22194400-22198400	Weak transcription	Brain Germinal Matrix	brain
24	chr7:22194400-22218200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:22194400-22219400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:22194400-22227200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:22194400-22232400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:22194600-22221200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:22195200-22198000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:22195200-22204000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr7:22195400-22197800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr7:22195600-22198200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr7:22195800-22197800	Enhancers	HMEC	breast
34	chr7:22195800-22198000	Strong transcription	Fetal Intestine Small	intestine
35	chr7:22195800-22198000	Strong transcription	Pancreas	Pancrea
36	chr7:22195800-22198000	Enhancers	NHEK	skin
37	chr7:22195800-22198200	Strong transcription	Lung	lung
38	chr7:22196000-22198000	Strong transcription	Left Ventricle	heart
39	chr7:22196000-22198400	Strong transcription	Esophagus	oesophagus
40	chr7:22196000-22201200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:22196000-22204200	Strong transcription	Dnd41	blood
42	chr7:22196200-22213800	Weak transcription	GM12878-XiMat	blood
43	chr7:22196400-22198000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:22196400-22198200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:22196400-22200400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:22196400-22200600	Weak transcription	Osteobl	bone
47	chr7:22196400-22213800	Weak transcription	Primary B cells from cord blood	blood
48	chr7:22196600-22198400	Enhancers	Brain Substantia Nigra	brain
49	chr7:22196600-22213600	Weak transcription	HUVEC	blood vessel
50	chr7:22196600-22214000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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